I think, Henry, you have got both the problem and solution in your message. I have also noticed the blobs in the can in which I've been soaking my brushes. I'm on the 4th door so it's been awhile since I've actually cleaned the brush with new thinner. I didn't notice (or have) this problem with bubbles in the beginning which was especially frustrating since the last door I did (when my skills were honed) looked worse than my rookie door. Since I posted today, I put another coat of (you guessed right) oil based poly, but I noticed, as you mentioned, a dry brush lightly applied, smoothed out the bubbles.
I'm glad I got this straightend out, I've been sanding the woodwork in the room with the 4 doors and plan to stain and finish it this weekend.
You all can take some small pride in my (hopeful) bubble freeness.
I'll then only have 6 more rooms of painted oak to uncover at which point I suppose never want to talk about paint stripping again...