Just curious, is there any reason you are using JQuery 1.7.1 instead of 1.8.2? It is supported, just genuinely curious.
As for your issue, can you tell us how you are doing this? Are you using an href=... are you using popup( 'open' );? If so how are you calling this?
Personally I have noticed a lot of issues with chrome and JQuery Mobile on the iPad. It's very inconsistent. I just tested the popups on the JQuery documentation with chrome on the iPad and didn't really have much of an issue. Have you tested these?
Note: I did see your issue on the JQuery documentation once, but refreshing fixed it. I still am not sure how it happened.