You’re correct: Post #1 shows it without 1990 in the title. Were that still true, we’d not be having the discussion nor would there need to be any answer.
That having been said, if I go by TheTVDB rules as we’re supposed to, it should work. Before answering here, I did a manual query via their web page. In both cases, ambiguous results.
I added ‘(1990)’ to the name and the ambiguity was removed.
So why the change? I did not completely understand the matching equation. The fault is mine.
Parsing ‘The Flash’ against “The Flash (2014)” yields a token match of 2 because the air-date year is not kept with the name. It’s stored elsewhere. That left 2 = 2 and it took it. It then goes and attaches it to the existing media item
Adding the year (1990) still walks through the same token match sequence. It has a 2==2 token match right up to the very end. Year matching 1990 != 2014 and boom new item. This is the well established rule we all know for movie remakes.
I did read about uniformity / consistency but until this ‘in hand’ instance of yours, and now my own, I had missed it.
Here, for reference, with no manual matches, no changes to Agent stacking or any other options whatsoever, this is how I now have it.
IMHO, it makes a lot more sense. Disambiguate both sides of the equation. Again… Sorry guys, I missed the basic math while deep in the rocket equations. 
/syno/tv/The Flash (1990)
sh-4.3$ ls -laR
.:
total 12
drwxr-xr-x 3 chuck users 4096 Oct 22 21:39 .
drwxr-xr-x 92 chuck users 4096 Jan 14 14:50 ..
drwxr-xr-x 2 chuck users 4096 Jan 14 15:05 'Season 01'
'./Season 01':
total 8162100
drwxr-xr-x 2 chuck users 4096 Jan 14 15:05 .
drwxr-xr-x 3 chuck users 4096 Oct 22 21:39 ..
-rw-r--r-- 1 chuck users 726778925 Dec 2 03:49 'The Flash (1990).S01E01.Pilot.avi'
-rw-r--r-- 1 chuck users 363342357 Dec 2 03:48 'The Flash (1990).S01E02.Out of Control.avi'
-rw-r--r-- 1 chuck users 363336911 Dec 2 03:51 'The Flash (1990).S01E03.Watching the Detectives.avi'
-rw-r--r-- 1 chuck users 363323438 Dec 2 03:52 'The Flash (1990).S01E04.Honor Among Thieves.avi'
-rw-r--r-- 1 chuck users 363394390 Dec 2 03:49 'The Flash (1990).S01E05.Double Vision.avi'
-rw-r--r-- 1 chuck users 363394666 Dec 2 03:48 'The Flash (1990).S01E06.Sins of the Father.avi'
-rw-r--r-- 1 chuck users 363304497 Dec 2 03:50 'The Flash (1990).S01E07.Child'\''s Play.avi'
-rw-r--r-- 1 chuck users 363402841 Dec 2 03:51 'The Flash (1990).S01E08.Shroud of Death.avi'
-rw-r--r-- 1 chuck users 363926237 Dec 2 03:50 'The Flash (1990).S01E09.Ghost in the Machine.avi'
-rw-r--r-- 1 chuck users 363344270 Dec 2 03:48 'The Flash (1990).S01E10.Sight Unseen.avi'
-rw-r--r-- 1 chuck users 363386911 Dec 2 03:50 'The Flash (1990).S01E11.Beat the Clock.avi'
-rw-r--r-- 1 chuck users 363376537 Dec 2 03:52 'The Flash (1990).S01E12.The Trickster.avi'
-rw-r--r-- 1 chuck users 363317147 Dec 2 03:50 'The Flash (1990).S01E13.Tina, Is That You.avi'
-rw-r--r-- 1 chuck users 363355624 Dec 2 03:52 'The Flash (1990).S01E14.Be My Baby.avi'
-rw-r--r-- 1 chuck users 363390208 Dec 2 03:50 'The Flash (1990).S01E15.Fast Forward.avi'
-rw-r--r-- 1 chuck users 363341392 Dec 2 03:51 'The Flash (1990).S01E16.Deadly Nightshade.avi'
-rw-r--r-- 1 chuck users 363344587 Dec 2 03:51 'The Flash (1990).S01E17.Captain Cold.avi'
-rw-r--r-- 1 chuck users 363319578 Dec 2 03:49 'The Flash (1990).S01E18.Twin Streaks.avi'
-rw-r--r-- 1 chuck users 363404590 Dec 2 03:51 'The Flash (1990).S01E19.Done with Mirrors.avi'
-rw-r--r-- 1 chuck users 363352330 Dec 2 03:51 'The Flash (1990).S01E20.Good Night, Central City.avi'
-rw-r--r-- 1 chuck users 363371833 Dec 2 03:49 'The Flash (1990).S01E21.Alpha.avi'
-rw-r--r-- 1 chuck users 363352579 Dec 2 03:49 'The Flash (1990).S01E22.The Trial of the Trickster.avi'
sh-4.3$