Holodeck is currently patched to version ST.25.20121210a.21. When you start up the launcher and choose Holodeck, it should say you are patching to that version in the progress bar prior to saying 'Engage'. It should also show on the top center of the screen when you load up the character select screen.
For those encountering this issue, can you let me know what version number you are seeing?
Okay guys, what I'm about to suggest "used" to work like a charm, I honestly don't know if it still does, but it's worth a shot, right?
So, you'll want to head over to your STO install on your system which by default is located here: C:\Users\Public\Games\Cryptic Studios\Star Trek Online\Live
Once there, locate and open up your "piggs" folder. There's a bunch of files in there with the extension of .hogg. Find the smallest one (unless you'd like to patch forever) and delete it. This will force another patch which in turn should "fix" the mismatch issue. Like I said, it used to work like a champ back in the day, so here's to hope!
If this trick doesn't work, let me know, I'll see what else I can do.
Best of luck all!
PS: Another trick to try is to uninstall Pando Media Booster as it's only used to download the game initially. View Pando as a uTorrent client, once you have the full game, you honestly don't need it anymore and that darned thing can in fact cause issues like these.