Sound volume dropping when punch in and out.

Hi,

I have an iMac 27" mid 2010 that I upgraded with 16GB RAM which runs Yosemite. I also have a focusrite sapphire pro 40 hooked to an octopre dynamic MK II. I am using Logic Pro 9.

When I record a band, after few punch ins, the software starts to glitch...

When I punch in, the punched stem is a bit quieter than the rest of the track, although nothing have changed in terms of levels.

Another issue is when I select the tracks I want to record before I press record everything is fine, then as soon as I press record all my tracks are record enabled apart from the ones I selected.

These issues occur always when the session is getting more tracks (approx 25/30 without any plug in just pure audio input)

Can someone please help!

Also I have a legitimate version of logic studio!

Thanks

Q.