I can't seem to reproduce this. I myself had 226 of 450 messages, and I was able to delete one successfully (so now down to 225/450). I may have to lower the number of messages to 225 just for testing (but this could impact everyone, because there is no per-user setting), but I'm doubting that is the issue at this point because I increased it (from 350 to 450) to give you ~100 slots of space and there was no improvement in the behaviour.
Can you try the same procedure in another web browser, or clear all cookies and sessions and cached data in your existing browser? There have been complaints about server-side sessions not always working correctly since the server move back in 2012, but it's something that's been very difficult to debug, and I'd guess that would manifest itself in the same way.
I'll also see about going through webserver error logs to determine if anything there is appearing. Going through the phpBB changelogs would still be a worthwhile thing to do. Things like this usually turn out to be actual bugs in phpBB.
Edit: Yes, I'm thinking this has to do with sessions. When I deleted a message myself, this was what transpired on the server URL-wise:
[25/Dec/2014:20:36:40 +0000] "GET /ucp.php?i=pm&folder=inbox HTTP/1.1" 200 5925
[25/Dec/2014:20:36:43 +0000] "GET /ucp.php?i=pm&mode=view&action=view_folder&f=0&st=0&sk=t&sd=d&start=200 HTTP/1.1" 200 4873
[25/Dec/2014:20:36:55 +0000] "POST /ucp.php?i=pm&mode=view&action=view_folder&f=0&start=200 HTTP/1.1" 200 2431
[25/Dec/2014:20:37:01 +0000] "POST /ucp.php?i=pm&mode=view&action=view_folder&f=0&start=200&confirm_key=PTC1L4HCK7 HTTP/1.1" 200 2240
1. Viewing my actual inbox
2. Viewing the 5th (last) "page" of my inbox. At this point is where I checked the checkbox, then pulled down the "Delete marked" selection and clicked Go.
3. Verification/confirmation page with Yes/No buttons. Chose Yes.
4. Page where I was told the message was deleted. You can see the confirm_key stuff.
Now here's what yours has (excluding all the /favicon.ico fetches):
[25/Dec/2014:16:21:45 +0000] "GET /ucp.php?i=pm&folder=inbox HTTP/1.1" 200 5979
[25/Dec/2014:16:21:59 +0000] "POST /ucp.php?i=pm&mode=view&action=view_folder&f=0 HTTP/1.1" 200 2399
[25/Dec/2014:16:21:59 +0000] "GET /style.php?id=1&lang=en&sid=573674c625dfbd6b399f99d9c133a25e HTTP/1.1" 200 2550
[25/Dec/2014:16:22:01 +0000] "POST /ucp.php?i=pm&mode=view&action=view_folder&f=0&sid=573674c625dfbd6b399f99d9c133a25e&confirm_key=1PVWH0G3EY HTTP/1.1" 200 6168
[25/Dec/2014:16:22:01 +0000] "GET /style.php?id=1&lang=en&sid=b68de00c3eac9cc21ac62570227c60cd HTTP/1.1" 200 2550
1. Viewing the inbox
2. Presumably attempting to delete some messages (can tell from the POST used here), or maybe this is the confirmation page.
3. Not sure what is going on here with the style fetch (maybe another tab at the same time?) -- but the important thing to note is the session ID in the URL (sid=573674c625dfbd6b399f99d9c133a25e
). That does not happen for me, and it almost certainly refers to an old/incorrect session, which phpBB will silently treat as "do nothing" if it doesn't exist (as I understand it), i.e. a no-op.
4. This would be the "messages were deleted" page, as confirmed by the confirm_key. However, again note the injection of a session ID in the URL (same session ID as mentioned in #3).
5. Another style fetch -- and this time for a different
So this is probably related to session problems, especially if you had no other tabs open to the nesdev forum at the time -- and if that's the case, this is the same thing thefox and some others have seen in the past. Sessions == cookies in this case. The server tends to have a lot of session files laying around leftover in /tmp, but which ones are for nesdev is unknown.
koitsu@gen /tmp $ ls -l sess_* | wc -l
I don't see any errors in the webserver error log during this timeframe that pertain to nesdev.
I would suggest clearing your entire browser cache, sessions, cookies, and restarting the browser and I bet the problem goes away (until it happens again in the future). Also, if you are using bookmarks of any kind anywhere, please make sure they do not contain the sid=XXX stuff in them.
As I read more about cookies and sessions on phpBB's site, I realise that their cookie mechanism only supports one domain, so I hope you're accessing the site as forums.nesdev.com and not something else? The webserver configuration doesn't give me insights into this, sadly.