I have a Schecter Damien Elite 6-string stock with EMG's and the pickup in the neck when switched to takes a second or two to "activate".

When it finally responds, it sometimes fizzles in and out while I'm playing.

I was wondering if I can get a few ideas as to what may be the problem and how to troubleshoot it.

I have already tried replacing the battery.
Do you have the old system, or the new fully solderles system?

It can only be one of two things regardless though.
1) There's a bad solder point(s) inside. This is about a 2 minute fix, you might as well redo the whole thing because it's that simple.
2) The quick connect isn't plugged all the way into the pickup. This is a more common problem than one would think. Just unscrew your pickup rings, and look at the bottom of the pickup. Make sure it's in all the way.

If you have a really really old EMG, then it could only be 1), since in the beginning they didn't have any form of quick connect.
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Thanks, when I get home I'll check it out. I had thought of the solder joints especially maybe the ones on the switch but the quick-connect never crossed my mind.
If you ever get crackling when switching pickups, or the pickups cut in and out, then you should check the 3-way switch. On the mechanical switches, sometimes the plates can push out over time so that they don't quite make a connection when engaged. If you gently push those little plates back together towards the middle then it will make a good connection again.

That's what I would check anyway.