I've added third CheckAllPairs(); into script and results are strange imo ;/

C:\pl>stuff.pl
Section A took 2.9140 CPU seconds
Section B took 13.4890 CPU seconds
Section A took 3.6350 CPU seconds
Section B took 44.2330 CPU seconds
Section A took 3.6450 CPU seconds
Section B took 46.9980 CPU seconds
[download]

oh, and I run perl v5.8.8 built for MSWin32-x86-multi-thread with 25 registered patches.