I have a vague memory of seeing a thread a while ago about something similar, and it was ultimately something to do with the activation server. I can't remember enough detail to be really helpful - or even to be able to find the thread again - but that would make sense, particularly as two people are seeing the issue with two very different software packages, with just about the only common link being the activation method (Waterboy - I'm assuming you're using FTActivation Manager, not floppy disk activation?).
This is a complete stab in the dark, based on a memory of a memory of a thread - but could it have to do with the internet connection? As in, perhaps when you start up, the activation manager tries to connect to the internet before starting. If it can, away you go as normal. If it can't, it will eventually give up and start anyway, and from then on everything happens fast - but in the meantime everything sits around twiddling thumbs and waiting. OP, is it possible that at home, your work laptop doesn't connect (or doesn't connect as quickly) to the internet, or that certain ports that the activation server might use to connect to the internet are blocked by your firewall? Likewise, is it possible Waterboy that your network connection is not too crash hot and occasionally it drops out at the critical moment?
Purely speculation at this point, but worth a thought perhaps!