I've had timing chips with the velcro strap before and don't ever remember them being a problem. I certainly don't wear long socks, just normal sports-type ankle socks, and it sits quite nicely on top.
If you're socks are really short (the trainer-liner type?), maybe wear something to protect your ankle, I'm thinking something like a sweat band. If you do the velcro strap up fairly snugly on top of that, it shouldn't move around or rub.
Edited: 06/09/2009 at 12:13