Does the freeze include the effects? I thought it only froze the vst instruments. It's strange because even when I've frozen all the tracks, there's still skipping (probably about 40+ tracks).
Think of "freeze" as temporary pre-rendering, because that's basically what it is. It renders the frozen track with all the effects applied so that the CPU doesn't have to bog down by applying the effects in real-time. yes it does render any applied plug effects as well.
You may (not so) simply be skipping because of computer performance issues. 40+ tracks is a lot of tracks, even pre-rendered. While most of today's computers should have the throughput to handle that, bottlenecks can crop up.
First I'd make absolutely sure you have o viruses, trojans, etc. infecting you computer.
Second, I'd make sure your hard drives are properly defragmented with all garbage can and temproary files deleted first.
Third, I'd isolate the computer form the Internet while using it as an audio device (there's rarely any need to be doing both at the same time).
Fourth, I'd remove - or at least deactivate - any and all memory TSRs such as anti-viral software, firewalls, weatherbugs, etc. that you don't absolutely need running while you're working the audio. Of course the same is true for other applications.
If all that is done and you're still skipping, then you might need to look at checking to make sure your memory is all working OK, that your hard drives are giving proper throughput, etc. If possible, make sure your project and data drives are on separate data buses and are the first slot in their bus.
If you are running MS Vista, back-grade to WinXP. If you have a smaller/older computer, sometimes all you need is a memory upgrade.
Finally, you can always reduce the size of your Cubase project by rendering stereo stems of parts of the project when you're done with them. For example, let's say you have 8 drum tracks and a bass track, Ge them right in the mix, mix them together, and render them as a stereo rhythm stem. Youv'e now dropped 9 tracks to 2 tracks.
G.