Hello,
JoomSEF NEVER generates URLs starting with index.php/...
Either you have not JoomSEF activated or the component where you are experiencing this does not use JoomSEF handler.

I think the problem must have been in some component that cannot cooperate with JoomSEF.
Make sure to disable usage of JoomSEF handler for all componnets, where you do not have JoomSEF compatible extension installed. (then you can disable them one by one to see, when the problem starts to reappear)