I get a crash after combining runes as well. had in the area of 1300. Started combining since there is no delete to get the number down and off runes I don't want/need/too many of. At first it worked fine. Then after combining about 10 or so times, it's been crashing after every combine.
if it matters this is when it started crashing and how I was combining:
uncheck tier 1, tier 2
pick utility from the drop down
close glyphs(only one open for me other then quints)
drop two quints in
rune moves across to screen under a retrieving data from server message box (sometimes this doesn't happen)
*BOOM* CTD, message box pops up saying launcher experienced an error and shut down
rinse, repeat = crash every time so far
so not every time, I just was able to combine twice on one restart... but still pretty close to every time.