Is that what's happening to me?

Maybe.  This condition only happens on a trace trap, which is caused by
the single-step flag.  I don't see why GDB would be setting the
single-step flag in the cases you mentioned, but I have observed it
doing so before.  I also doing understand why it would be touching a
system call with it set in that case.

Basically, I don't know what GDB is doing, and I don't really have time
to figure it out, so I can't answer that question.

BTW, when did you last update your copy of GDB, and how?  The problem
you mentioned sounds very much like you didn't recompile it after I
recent change I made that shifted some values in struct reg.