I did some Googling of the forum because I remembered people reporting recordings starting one measure late. Most of them were about MIDI and were very old like SONAR 5-6, but there was at least one about audio in X1. Unfortunately, that one seemed to be affecting only a limited number of people and just petered out without any real resolution.
 
One thing you might try short of a complete uninstall/reinstall of SONAR is deleting/renaming your AUD.INI file and letting SONAR build a new one. You'll find it in C:\Users\<username>\AppData\Roaming\Cakewalk\SONAR X3 Producer
 
 

Update: I called Cakewalk yesterday evening.  They needed to look into the issue further and will get back to me hopefully today.

UPDATE: I was advised by Cakewalk to completely (and thoroughly) uninstall X3 and reinstall.  So I did, and things are not better; the recorded audio delay still existed.  So I uninstalled ALL versions of Sonar (X1, X2 and X3) and wiped the registry clean. as instructed by Cakewalk.
 
I just tested it now...and...
 
...the delay in recorded audio is still there!  Seriously...this is %$@#&@ ridiculous!!!
 

 
EDIT: If I change the metronome to MIDI notes instead of audio, the delay goes away. So what the heck does that mean?

Hi 2:43
Yeah, still no idea here what's going on. I've been trying to find some time to get on the phone with support but haven't gotten around to it. I'll let you know if I find anything out and please do the same if you get any good info.
 
Dean

2:43 AM, it appears you're overclocking your CPU. I'm not sure if that (or some setting related to it) could cause this, but I wouldn't rule it out given how unusual the problem is. How hard would it be for you to reconfigure for rated speed?
 
 

brundlefly
2:43 AM, it appears you're overclocking your CPU. I'm not sure if that (or some setting related to it) could cause this, but I wouldn't rule it out given how unusual the problem is. How hard would it be for you to reconfigure for rated speed?

You're right! I am indeed overclocking with much stability. Swapping back to default CPU/System parameters is relatively easy, so I went ahead and did just that and proceeded with the test. The result is the same: big delay in the recorded audio.
 
This is some seriously funky stuff going on here; impossible to narrow down. The "issue", even if it wasn't a true bug, was gone in X2a but only later in the game. I submitted a bug report of this very thing for X2a! Little did I know that Cakewalk would never release an X2b. But then the issue seemed to go away by itself.  I reported in this thread that X2a worked well; no issues. However, now in X3e, the issue seems is back! So now it's worthy of me to try to figure out what setting change--what tweak--I did in X2a that cured the problem.
 
This is the best thread of yesteryear that I could find on the exact same issue.  The issue has been around since 2011 and maybe earlier (I think some threads reporting count-in problems date back to 2008). See http://forum.cakewalk.com/tm.aspx?m=2413605&p=3.  Brundlefly's been helping with this topic since at least 2011! Thanks for sticking with it!  Unfortunately, for all users, no complete resolutions nor the identification of the problem have been mentioned since then.

Yeah, that's the main thread I was referring to earlier. Did you ever try renaming your AUD.INI file or switching driver modes? You might also try enabling UseHardwareSamplePosition=1 in AUD.INI.

Did a test counting 12345
When I playback its starts at 5 so no issue here.