I will need to see the XML of what you’re playing as well as whether or not you’re using HW transcoding but looking at your logs tells me your Synology is pretty seriously overloaded for I/O. 121 seconds to query the database = 2 minutes which is not acceptable 
You also have autotagging enabled (just added a lot of photos ?) and it’s throttled due to overload.
How much memory is installed? Hardware transcoding needs memory. With the amount of activity from other tasks, I wonder if there’s really enough .
What happens if you cancel photo library scanning?
How many photos did you add?
Would you please cancel any and all scannng then hover over Libraries, click the ellipsis, and click “Optimize Databse” then restart PMS?
Jun 11, 2018 16:18:52.791 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 26696
Jun 11, 2018 16:18:52.793 [0x7f2c143ff700] WARN - AutoTagging: the service is currently throttled, skipping item 16871
Jun 11, 2018 16:18:52.794 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 16805
Jun 11, 2018 16:18:52.798 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 16898
Jun 11, 2018 16:18:52.798 [0x7f2c143ff700] WARN - AutoTagging: the service is currently throttled, skipping item 8643
Jun 11, 2018 16:18:52.800 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 8642
Jun 11, 2018 16:18:52.802 [0x7f2c143ff700] WARN - AutoTagging: the service is currently throttled, skipping item 8645
Jun 11, 2018 16:18:52.804 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 13924
Jun 11, 2018 16:18:52.806 [0x7f2c143ff700] WARN - AutoTagging: the service is currently throttled, skipping item 15674
Jun 11, 2018 16:18:52.807 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 13925
Jun 11, 2018 16:18:52.809 [0x7f2c143ff700] WARN - AutoTagging: the service is currently throttled, skipping item 15675
Jun 11, 2018 16:18:52.811 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 16170
Jun 11, 2018 16:18:52.812 [0x7f2c143ff700] WARN - AutoTagging: the service is currently throttled, skipping item 12788
Jun 11, 2018 16:18:52.814 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 6512
Jun 11, 2018 16:18:52.815 [0x7f2c143ff700] WARN - AutoTagging: the service is currently throttled, skipping item 20734
Jun 11, 2018 16:18:52.817 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 21594
Jun 11, 2018 16:18:52.819 [0x7f2c143ff700] WARN - AutoTagging: the service is currently throttled, skipping item 20755
Jun 11, 2018 16:18:52.820 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 20756
Jun 11, 2018 16:18:52.822 [0x7f2c143ff700] WARN - AutoTagging: the service is currently throttled, skipping item 12715
Jun 11, 2018 16:18:52.824 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 12732
Jun 11, 2018 16:18:52.825 [0x7f2c143ff700] WARN - AutoTagging: the service is currently throttled, skipping item 12741
Jun 11, 2018 16:18:52.827 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 12749
Jun 11, 2018 16:18:52.828 [0x7f2c143ff700] WARN - AutoTagging: the service is currently throttled, skipping item 16129
Jun 11, 2018 16:18:52.830 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 8865
Jun 11, 2018 16:18:52.832 [0x7f2c143ff700] WARN - AutoTagging: the service is currently throttled, skipping item 20200
Jun 11, 2018 16:18:52.833 [0x7f2c210d7700] WARN - AutoTagging: the service is currently throttled, skipping item 20921
Jun 11, 2018 16:19:01.680 [0x7f2c13e23700] ERROR - Throttle: timed out trying to read chunk 17
Jun 11, 2018 16:19:14.084 [0x7f2c14111700] ERROR - Throttle: timed out trying to read chunk 5
Jun 11, 2018 16:22:46.866 [0x7f2c1326b700] WARN - Waited one whole second for a busy database.
Jun 11, 2018 16:23:13.179 [0x7f2c1326b700] ERROR - Failed to delete session directory (boost::filesystem::remove: No such file or directory: "/volume1/Plex/Library/Application Support/Plex Media Server/Cache/Transcode/Sessions/plex-transcode-x3mfzx2o9w55bg0sgplul3di-405253b5-29f5-4edf-a711-f476551d9506/chunk-00101")
Jun 11, 2018 16:23:13.305 [0x7f2c28911700] WARN - SLOW QUERY: It took 121270.000000 ms to retrieve 10 items.
Jun 11, 2018 16:23:13.796 [0x7f2c14111700] ERROR - Throttle: timed out trying to read chunk 115
Jun 11, 2018 16:23:38.698 [0x7f2c14111700] ERROR - Throttle: timed out trying to read chunk 11
Jun 11, 2018 16:24:04.916 [0x7f2c22e23700] ERROR - Failed to delete session directory (boost::filesystem::remove: No such file or directory: "/volume1/Plex/Library/Application Support/Plex Media Server/Cache/Transcode/Sessions/plex-transcode-rvhpwbaremn6wecjpjvklz0k-0f0c1efc-7e7f-47f9-b656-02440a21fe84/chunk-00013")
Jun 11, 2018 16:24:05.158 [0x7f2c216b3700] WARN - SLOW QUERY: It took 210.000000 ms to retrieve 39 items.
Jun 11, 2018 16:30:03.685 [0x7f2c13847700] INFO - AutoUpdate: no updates available
Also you are showing these back to back which is a bad sign of a fragmented database caused by adding a lot of items (e.g. Photos) to index.
Jun 10, 2018 18:44:10.316 [0x7f81f788f700] WARN - Held transaction for too long (../Library/MetadataItem.cpp:7224): 16.940000 seconds
Jun 10, 2018 18:44:12.808 [0x7f81fe11d700] WARN - Took too long (0.190000 seconds) to start a transaction on ../Library/MetadataCollection.cpp:172
Jun 10, 2018 18:44:12.808 [0x7f81fe11d700] WARN - Transaction that was running was started on thread 0x7f81f788f700 at ../Library/MetadataItem.cpp:925
Jun 10, 2018 18:44:13.556 [0x7f81fe6f9700] WARN - SLOW QUERY: It took 480.000000 ms to retrieve 38 items.
Jun 10, 2018 18:44:14.465 [0x7f81e91a5700] WARN - SLOW QUERY: It took 550.000000 ms to retrieve 40 items.
Jun 10, 2018 18:44:16.886 [0x7f81e91a5700] WARN - SLOW QUERY: It took 910.000000 ms to retrieve 30 items.
Jun 10, 2018 19:02:12.976 [0x7f81fc7ff700] INFO - Library section 1 (Movies) will be updated because of a change in /volume1/Media/Movies
Jun 10, 2018 19:02:20.928 [0x7f81e6e7d700] WARN - SLOW QUERY: It took 210.000000 ms to retrieve 38 items.
Jun 10, 2018 19:02:21.086 [0x7f81e82ff700] WARN - SLOW QUERY: It took 280.000000 ms to retrieve 1 items.
Jun 10, 2018 19:02:21.166 [0x7f81e9493700] WARN - SLOW QUERY: It took 370.000000 ms to retrieve 30 items.
Jun 10, 2018 19:02:21.964 [0x7f81e9493700] WARN - SLOW QUERY: It took 220.000000 ms to retrieve 75 items.
Jun 10, 2018 19:03:13.975 [0x7f81e9781700] ERROR - QueryParser: Invalid field 'onlyTransient' found, ignoring.