Project was going along smoothly for weeks, but now I get "Warning - Dropped Frames"
 

This message comes up repeatedly.

I can access my scratch disk just fine on my my desktop but playback in FCP is going haywire. It'll play the clip in 2 second spurts and each time it'll only play the audio from the left or right channel, never both. Messing with playback quality is not working either.

I trashed the preferences earlier when there was an issue with another project I was working on (a totally different issue), but I doubt trashing prefs would do anything so wrong.

I'm working off a 500gb drive, connecting to my computer with a firewire 400 (800-400 wire).

and now I'm back in business. I was trying some last ditch desperate efforts and it worked. All I did was switch my scratch disk from my external to my system drive and then back. This is so weird that I'm afraid of getting excited.

Possibly a lot of fragmented render files strewn across the Render target disk. As I near project completion, I "blow out" render files using Render Manager and re-render to get the most seamless renders possible.

The issue has returned, but I sort of figured out the problem-- the audio. If I delete the audio from any of the clips they play just fine, but when I leave the audio in, it gives me dropped frame issues.

Possibilties:
Fragmented files - transfer the entire contents of the drive from the drive in question, reformat the drive and transfer them back.
Drive failure - The drive in question is on it's way out. Transfer the files immediately and run a drive maitenence program like TechTool. This won't fix a mechanical failure but you'll be able to see something is up.
5400rpm drive - don't use these for video editing if you can help it. They will work until the drive starts to fill up.
FCP is just too darn sensitive - sometimes the program registers dropped frames when it can't be seen. if you are not experiencing any playback problems you can turn off the alert message in the user preferences.

It seems that if I switch the audio from 48 kHz to 44.1, it will play perfectly. If I continue to do this project at 44.1 will I run into any issues when I complete it and burn it to dvd?

That doesn't make any sense at all; 48Khz is the standard that any FCP timeline is looking for, if it's any other bitrate it will want you to render it. I've never even heard of it going the other way.

It sounds to me like you may have a corrupt project or other deeper files that need to be fixed up.

Try downloading Digital Rebellions FCP Toolkit and see if it's maintenance and cleaning routines get you fixed up; chances are it will.

I've seen this problem when the storage disk gets too full, or as another poster points out, gets badly fragmented. If you get near 90% full you will encounter problems....