(Super-late reply, yay!)
I'm slowly in the process of trimming away old stuff and optimizing
the speed execution of everything else - it's true that JD isn't
exactly a speed champion now on slower CPUs (both because the N1
spoiled me and because I focused too much on adding features and too
little on possibly-premature optimization :) )
However what you describe doesn't seem normal at all... If it's not
the usual 'corrupted apk' problem that gets fixed via a reinstall
(worth a try), it's probably due to some problematic interaction with
some other app. For example recent versions of the 'SuperUser
permission' (as found on modaco and cm roms) have been causing lots of
trouble and slowness - and most recently outright malfunctioning of
"root" apps.