weird run-times with pg_autovacuum

Hi all!
I recently started using pg_autovacuum instead of scheduling vacuum
analyzes in a system that needs to be taken to production soon.

However, I have noticed something funny that happens while using this.

sometimes, some database operations take an unreasonably long time to finish.
I have not been able to pin the problem down to any specific cause and
the problem is also not reproducible( atleast I don't know how to make
sure it happens again ) but what happens is that some queries take an
unreasonably long time to finish.

pg_stat_actiivity showed some selects running on a table with ~90k
rows at one such time of weird behavior(they ran for a long long
time).

Is it possible that pg_autovacuum is auto vacuuming that same table at
that time and there is some unnecessary waiting involved because the
table is locked?

I am a complete newbie to postgres and I am throwing darts in the
dark, but can anyone give me any idea of where and what to look for?

thanks a lot!
ps