I suggest you contact customer support. You didn't say which version you're using - which is quite important as there have been a number of fixes related to Verilogin.
You could always turn off the Full Place & Route option, so that it doesn't attempt to fully route the schematic. You could also decrease the density - it's a slider on the form. But without knowing what the real issue, it's hard to be sure. 1024x1024 should be OK for 40k components.