I'm not sure uncompressed audio is expected to work on the old archoses. Does mp3 work well?
Things you could look at (in no particular order):
* Hardware issues, possibly with the hard drive. Does it behave strangely over USB?
* Bad settings that reduce available memory for buffering too much. Do you have the database, dircache, or voice files enabled? If so, try disabling them and see if that improves things.
* A bug in recent versions. The JBR isn't used by many people these days, so it's probably not impossible that there are some undetected issues in recent builds. Which version have you tried? It might be useful to test with older versions (you can find those at
http://download.rockbox.org/release/). Note that recent versions definitely use more memory (the cost of more features...), so differences here might be due to that and not to a "real" bug.
Switching to an SSD should definitely make the entire system more responsive, and possibly also improve battery life.