What's Arena? And what does it offer?
Sorry for ruining your post just in the second comment :(
Until reading this thread, I'd never used the Arena filtering feature. (Arena isn't the best program for working with databases.) I downloaded your last 50 games, and I was able to duplicate your problems. I've also looked at the contents of your 50-game PGN file, and I too can't see exactly what might be causing the problem.
I did confirm that if I strip out the comments, the Arena filtering feature seems to work OK, except for the initial starting position bug.
I'll also add that Scid vs. PC is able to filter these positions correctly without having to strip out the comments.
If you want to strip out the comments in your PGN file, there are several ways to do it. One way is to use Scid vs. PC - You can open the PGN file, then go to "Tools --> Export All Filter Games --> Export Filter to PGN". Then, in the "Exporting" box, for the option "Export comments?", click on "No".
A couple of other ways to strip out comments are mentioned in this link:
https://www.chess.com/forum/view/general/webpage-to-remove-comments-from-your-pgn
how to search database by position in arena
Eh, just go into the Arena "Help" and search on "filter games". Some basic instructions will be there. In general, just open up a PGN file, then click on the "filter" button as shown below:

Then click on the Position tab, and add the position you're searching for. Then click on the "Filter" button, and there ya go!
Hi
I recently downloaded my game archive from Chess.com in PGN. I then opened it with Arena software, and started applying filters (by position),
I found out that the results of the filters were wrong. For example, when I looked for the initial position, no results were yielded. I then looked for the French Defense position (after 1.e4 e6) and just a few games were shown (I am a French defense player), some of which were not even French Defenses.
I wanted to know if it has happened to you, and how to fix it. The software read other databases correctly, the problem is just with mine. I tried comparing the formatting of the PGN text, but I didn't find any difference between my database and other databases which worked perfectly (apart from the time signature. Could that be a problem?)
Thank you very much