Wondering ...

I have 2 rear wheels -- they are not the same wheel. During the winter I have been using one wheel as my "trainer wheel" and the other wheel as my outside wheel. Until yesterday, I would move cassette from wheel to wheel, depending on which one I was using. Also, I would have to make minor rear derailleur adjustments between wheels (I believe the dish is different on each wheel, but adjustments minor and no big deal).

Anyway, yesterday I put a new cassette on my outside wheel and a new chain on the bike, adjusting the new cassette/chain combo to my outside rear wheel. Then I swamped wheels, putting my old cassette/trainer wheel on bike to ride indoors. It was such a mess! The derailleur didn't shift to all cogs, it was noisy, and when I did get it to shift to all cogs it would "jump or pop or something" when I stood, especially on the 53x13. Is this an alignment problem or a old cassette/new chain problem?!