MetaMod *should* work exactly the same with or without SEF URLs turned on. The magic of Joomla SEF URLs is that internally, you still get access to variables like $option and $view and $id, even though they don't appear in the publicly displayed URLs. It's clever. In most cases you can use exactly the same PHP rule whether SEF is turned on or off.

Thousands of people are using this on their sites in both modes, so generally it does work.

So I am a bit mystified as to why it seems to be making a difference for you.

Could you perhaps post the recipe you're using, just in case I can spot something in it?

Also, can you try turning on Advanced Debug mode in MetaMod, and see if the output from that gives any clues as to what's going on when you turn SEF on or off? (or add suffixes).

Cheers,
Stephen