true clockwork is more likely to create a problem then RA regaurdless of version.
i've mostly wiped and flashed with RA but when RA updated past 1.8 there seemed to be reports of problems. and there was a new version coming out every other day. this may have just been some compatibility with 0004 versions or even other phone models. not sure but i decided to switch to clockwork for my last couple of flashes.
clockwork 2.5 worked fine for me no issues. 2.6 the latest one gave me all kinds of issues. every reboot from recovery gives me lines across my screen (not really an issue, just something that happens). would not wipe dalvik, well it never really does a good job of that anyway. but this version actually locked up on dalvik wipe a couple of times, had to pull battery. it also didn't seem to wipe user data correctly either. some apps started to dissappear. could not update some apps, including rom manager. uninstalling didn't seem to help as the market still didn't want to install them.
so yeah, back to RA for me.