A couple of things to check.
1. Are you sharing the data with VFP8 or is it a separate dataset. I seem to remember a problem with sharing the same data between VFP8 & VFP9
2. There are differences in VFP9 with Indexes See : Considerations for Creating Index Expressions in VFP9 help
3. Is the virus scanner excluded from the VFP9 dataset & the VFP9 Program directory.
4. I remember some time ago where upgrade performance issues were overcome by recreating the tables in VFP9 then copying them back, probably had something to do with item 2.

>interestingly in develop the screen run normally but slowness only happens in runtime!

Is the dev local or networked, is the runtime networked.