Hi zackiv31,
Really there is little I think link-assistant can do to fix this for you (it is due to the large amount of data being processed by rank-tracker and your own PC's lack of available memory).
The options are:-
a) Buy a more powerful computer (not a sensible option really... of course).
b) Run your 45,000 keywords in groups of a smaller quantity as I suggested (from your own experience, it sounds like 15,000 per time might be possible without your computers lack of memory causing the software to crash i.e. run as 3 groups / 1 group per time).
c)Remove keywords which are not truly useful for you to be tracking ranking position for... as in reality those keywords just never get searches / bring any traffic at all, more than once in a blue moon (or once ever in history perhaps) i.e. 45K keywords, is a lot to be actively targeting a site for - so perhaps it is worth reviewing the need for 45K keywords as well.

I really suggest that you take these options, rather than hoping / expecting that a software supplier can change their program to fix a PC out of memory problem.
I hope comments are useful...
Cheers - Asiaplay
PS: You should be able to run / make reports, when you have collected data which is not corrupted by crashing due to trying to run too many keywords in one run - so try grouping keywords, not crashing and you should get reports as well...