I thought banks might be a little sniffy about using clients using VPNs, but it doesn’t seem to be the case. At least not with the two Canadian banks I deal with.
As always common sense helps: If you log on from–say–the US, and then log on from India you are still likely to activate extra security. Personally I don’t mind when security protocalls spring into action–at least you know they’re taking your security seriously!