Dose turning on "Do not scan system libraries" have any major effect on security?
It's perfectly safe, and that's why it's actually the default.
I'll check how many files are scanned after boot-up tonight
That would definitely be helpful. Maybe there's a background process that's scanning your hard drive on system startup, trigerring exhaustive scans by avast. BTW what OS are you using?
Are there any known issues with Lock ‘n’ Stop firewall and Spyware Doctor?
There shouldn't be any issues.
Do I even still need Spyware Doctor?
That's a good question.
I personality don't like Spyware Doctor, but maybe it's just me (I hate their business model - I find it basically a rip-off). But the program can do the job (if you have the paid version, that is).
Thanks
Vlk