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.

Hi,talked with an apple technician who told me the leds on memory boards lighting up is normal , when going in and out of sleep and also with booting up and shutting down...
The leds lighting up are marked as: Q3A1, Q3A2, Q3A3 and Q3A4, situated right of middle on memory board..This lighting up is accompanied by a click..and a winding down or winding up sound of a motor...
Your machine has this as well??

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