Flame always hit harder than fireball, regardless of in siege or not, unless you're comparing Flame non-crits to fireball crits.
The extra factor you have to consider for siege is shields/damage reductions. Mages, Wardens (nature crystal) and C/M have shields that absorb damage equal to a % of their HP. So if you Flame first, their shield absorbes part of that damage (or all) and your Flame seems to have critted for very little. Other classes have damage reduction CD's that reduce damage they take in a few seconds, so if you cast flame while it is in effect than follow up with fireball after it ends, than fireball may seem to crit more.
I did notice that Flame seems to crit very little in siege though... or is it just me?