@The_Weeze, when I installed the custom Hydro LG L55C rom, I noticed that apps on the sd card didn't show up either. I could very well be completely wrong with what I'm about to tell you, but when you move an app from the Internal Memory to the SD Card theres still application data saved on the phone. If you look at the size of the file before moving and after moving in your all applications list it greatly reduces but doesn't zero out. I think that what happens is, the apps aren't completely moved to the SD card. I think that some of the core parts of the application are usually saved on the phones internal memory with the bulk of the extras being on the SD Card. Now I could be completely wrong about that.
What I've found works best for me when flashing ANY rom, is to backup my essential apps with Titanium Backup. Then I backup my music, any rom.zips, and my clockworkmod backups to the Computer. What I do next is reboot into recovery. Wipe all data, cache, and delvik cache then proceed to flash the rom. When the phone reboots, I unmount the SD Card, erase all data, and proceed to restore my Music to the SD Card (here you could also restore your recovery but I have so much music on my 4gb SD that I'm really just trying to keep space.). At this point I run titanium backup and restore all my apps to the phones Internal Memory. At this point I move all the apps I can to the phones SD Card. I then restart whatever launcher I'm using (I personally use adw, GO seems to cluttered on these screens). I like to use Android Assistant and sdmaid to keep my phone uncluttered, but using the method described above I have no problems accessing my apps.
I wrote this without ever using a VM Slider or this rom in particular. But, IME with Hydro Roms the method above seems to work best. My advice is to temporarily fill you internal memory up when you flash, and try to start from scratch...just backup/restore with Titanium Backup. Good luck!