Logic Pro 9 L9 - Strange Behaviour?


I have almost made the switch - I am moving from DP - and in order to keep $$ coming in and studio workflow consistent - I have been duplicating all projects from DP into Logic and sort of running my own beta tests....
First, let me thank all of those who have helped me in this transition - this forum has been great ...
I actually tracked my first couple of sessions the other night in L9 - I guess I really had a chance to work with it - as opposed to just fiddling around, mixing, adding plugs, etc. - so I noticed a coupe of issues that I deem pretty serious - as compared to my working with DP - so perhapssome folks can lend some assistance.

First - I am running a Mac Dual Quad (octa) 2.8 with 16gigram, interfaces - MOTU 2408mkIII, MOTU 24i/o and a MOTU 308 - PCI-424E, clocked to an Apogee Rosetta 800
MIDI - MOTU MTP A/V, MOTU midiexpress, about 10 outboard synths and modules, 1 Mackie MCU, and 2 x Controller XT's.
System with DP has been pretty rock solid - really no issues, and I didnt really have to change anything other than the system boot on the mackies to the Logic controller mode.

1. MIDI Sync - while tracking and/or listening, etc. - every once in a while Logic will stutter... and the tracks related to the external MIDI synths will now play out of sync with the audio tracks already recorded, loops and VI tracks in the project > stuttering is not good.
As I mentioned its happened several times while tracking - which has really sucked. A simple stop and start gets things back in order - but for a professional DAW that I intend to use in my day-2-day... that really is unacceptable. I find it hard to believe that I am taking my system - I would say I had perhaps, 10 audio tracks, with maybe 2 or 3 plug ins assigned at the time - (1) record enabled audio track, and maybe 1 or 2 VI's assigned playing MIDI data as well. The MOTU MIDI interface - has been a workhorse for me for quite a long time - and I don't suspect that as the culprit.

2. Stuttering/hiccup - again, I was dropping a rough mix of the same project to send off to my client in Nashville - Since I use a Dangerous 2 bus for summing, I don't "bounce"... I send my tracks in stems out the summing box, then routed through a TK Audio BC1 bus compressor, and back in through the apogee, and drop them in real time - While I was recording the stereo mix... Logic about 3/4 of the way through the song hiccuped/stuttered - whatever you want to call it... skipped maybe more appropriate...

Its not a constant thing - but man it really makes me question the reliability.
I was reluctant to make the switch - but after messing with L9 for a while - it really started to get my creative juices flowing again.. and I have been really excited about making the move - but I must say, while DP and MOTU have their issues and flaws... My DP5.13 has been very stable and never left me in the lurch - especially whilst tracking.

Any ideas?