yes i have the same problem as that, some think it is my IT band that i dont roll enough with the foam roller, getting some rocktape has helped me quite a bit. i went for an MRI and they said it was an ACL sprain and i had swelling in my knee joint. my physical therapist wasnt that convinced and thought it was still my IT band.

click on my link below and try some out, if you would rather like a small sample, email me and i can send you some. you might need a few applications to start noticing an improvement though.

this stuff has really worked well for my knee, i now use it on my calves and IT band as well.

I hear ya, I get that same kind of knee pain more on the trainer than outside on a real ride.  I love the convenience of the trainer but the fit/position just isn't the same as having your bike out on the road.  I end up having to make a few adjustments to my positioning when on the trainer versus out for a real ride.  I've had the same sort of knee pain and changing up the position a little has helped...the trick is getting things put back in place when you're ready to get outside but it's do-able.

I've also realized that when I'm out on the roads I ease into the workout better and warm up just by heading through town on my way to open roads.  However, when I'm on the trainer I didn't used to take the same amount of time to warm up and I know that plays a role in the pain too.  I started warming up my legs more before getting on the trainer and starting the workout, that has helped me more than anything to keep the pain/inflammation down.

Do you do any regular strength training?  It's good for injury prevention and doesn't have to be anything crazy.  Exercises like light squats, lunges, step ups might be good for you.

At first I was moving around my cleat position to see if that would help but I ended up putting it back to where it was initially.  What ended up doing the most good was lowering the height of the saddle and moving it forward just a little.  It put me at a slightly different angle and that seemed to be all I needed.  Everyone will have a different solution though so when you make the adjustments just do them one at a time, it'll be easier to figure out what does the most good.  It can be a bit of a hassle but my thinking is that if it keeps me pain free and I can be more comfortable on the bike then I'll get much more out of each workout.

Be sure to mark (with tape or something) what your original positions are so you can always go back to them.  Good luck!