I think i've  experienced  a similar  issue to this  
myself, using version 3.00 on Windows 98, also  with 
a "large"  site of  around 70000 links - this takes 
some time with a modem

obviously I will upgrade to the new  version first of 
all, but if there is still the same issue (maybe  not  
as sever) then I'll keep looking into possible causes 
and solutions that can be improved with general system 
housekeeping and I'll post anything that I come up with