Latency Between Outputs After Project Conversion From Logic Pro 9

Question

hiya!
i am experiencing a bizarre kind of latency – between outputs. for example, audio assigned to stereo outs 13-14 will leave my system 120 or so ticks after audio assigned to mono outputs 3 or 4. sometimes mono outputs are out of sync with one another too. there's no apparent rhyme or reason, and the latency itself seems to shift – even with plugins turned off and removed from the channel strips. if i have an aux that's outputting to channels 7-8 and do a send to an aux that outs to 13-14, this audio should be perfectly aligned, but it just isn't.
i experience this problem in sessions converted from logic 9 to logic x, though sometimes it seems to happen within sessions started in logic x. i can't for the life of me figure out why it's happening, but do believe there's some sort of error being introduced in the conversion. i can't find anything anywhere on the internet about it.
one temp fix i found was to insert an I/O plugin into the problematic aux, turn it on with an out assigned, then turn it off. sometimes that's worked, and sometimes it hasn't. i've been able to use delay compensation on certain tracks, but it's not an exact science, and sometimes the compensations themselves need to change in order for the tracks to sound aligned. it's beyond aggravating. in some situations, i've had to re-record entire sessions. not tight!
to be clear, this is not about monitoring latency, or having to slide tracks into alignment after recording, or the waveforms on the screen not matching up with what i'm hearing. this is not about plug-in latency. the situation i'm describing happens when plugins are entirely removed: audio that is supposed to be leaving logic at the same exact time via different outputs is somehow not aligned.
my signal chain:
logic pro x.0.7
mac pro quad core (trash can) into -->
apogee symphony 16x16 -->
neve 5059 16x2x2 -->
api 2500 -->
back into the symphony
i've been assured by both apogee and neve and sweetwater that this is not their issue--it's logic pro x. i'm inclined to agree, since it seems to be happening before the audio leaves logic.
please help! many thanks for anything!

Answer 1

godmodeinternet wrote:
thanks for your reply!
to answer some of your answers:
-i have all my channels go through auxes, in all projects, but i did attempt to route audio straight off the channels and encountered the same situation i described above.
-plug-in latency is likely set to ALL at all times, since i often track while in the 'mixing stage'. this is how i've always done everything.
ugh. the worst!
do you think there's anything in environment i might be able to swap around that might have gotten screwed up in the conversion?
thanks again.
I don't think it's an Environment issue, however, quite a few people have reported some corruption when importing Logic 9 projects, it usually takes the form of random Inspector Settings for Delay/Velocity and Preferences/Audio - Recording Delay  being set to something other than 0 <zero>. This doesn't sound like your problem. Also sounds like your Plugin Latency setting (ALL) isn't the problem.. although if you're recording while mixing it should be set to Audio & Software instruments.
Have you used your hardware system successfully on an earlier version of OSX and Logic 9?  If so then the answer is apparent, especially so if you notice it on projects started in Logic-X (current system) although it my take a certain level of project complexity before it shows up.