Hello,
Why not base PuTTY Portable on PuTTY Tray, instead ? I'm using it right now (just replaced the original putty.exe by the one from PuTTY Tray), and it works like a charm (most likely because of the smart design of PuTTY Portable).
PuTTY Tray is there: http://www.xs4all.nl/~whaa/putty/