I think I've spotted a repeatable bug with recording in loop mode. Here's how to repro it on my machine:
 
1. open a new blank project.
2. Insert an audio track.
3. enable the audio metronome and set a 1 measure count-in
4. set a loop region and enable the loop. I use a two bar loop, but any size will work.
5. begin recording audio on the track you created. It doesn't appear to matter if you record more than one cycle of the loop region.
6. Stop recording and listen back.
 
On my system this always results in audio being about two beats late. The strange part is that the clip shows the correct time region, but the recording actually started during the count-in. For example, if I were to count beats into a mic (just saying "one, two, three" etc, one count per beat) starting on the first beat of the count-in and continuing for 2 bars (in 4/4), I would expect to record the numbers 5-12 and NOT record numbers 1-4 (they occur during the count-in), but that's not what's happening. What gets printed is numbers 3 through 10, i.e. the last two beats of the count-in are recorded and the recording ends two beats early.
 
If I'm recording without a loop or with no count-in it works fine.
 
Thanks,
Dean

Are you using X3e? It included several fixes that related to loop and punching issues when recording.

Hi Craig,
Thanks for responding. I am using X3e build 352. Any chance you've had a moment to try this? I'm curious to see if it happens on anyone else's system or if it's unique to mine...
 
Dean

I just did this.  And yes, I get a 2-count delay occurs.
 
Man, I thought it was fixed!!!

I've never experienced this because I don't use a count-in for a loop. I always set the now time somewhat before so that the song itself provides the count-in, and I can get "in the groove."

Time for a bug report.

I just tried what I thought your steps were but couldn't get it to act up. Here are your steps, with more details on what I did. Steps 1- 3 were the same...I enabled the metronome for record only, if that makes any difference.

4. set a loop region and enable the loop. I use a two bar loop, but any size will work.
 
I set a two bar loop from measure 3 to measure 5.

5. begin recording audio on the track you created. It doesn't appear to matter if you record more than one cycle of the loop region.
 
I set the Now time to the beginning of the loop and started counting 1, 2, 3, 4 on the beat as soon as the countdown began. The now time didn't move during the countdown, then it moved and recording started.

6. Stop recording and listen back.
 
I stopped recording before the end of the loop, if that matters. When I played back, the clip started with 5, 6, 7, etc., as expected.
 
Then I thought maybe you meant that you had punch and looping enabled, so I tried that but still got the same results. Next, perhaps you had the loop starting at the beginning, so I tried that...but it still worked as expected.
 
I'm trying to figure out what's different about our two scenarios so I can reproduce it.

Yeah, something's missing from the recipe or it's system-specific. I can't reproduce it, either, and I can't imagine this wouldn't have been reported before now if it were widely experienced.

bapu
Time for a bug report.

 
This has been reported.  I know I reported this back in the X2 days, but I think it was user-error rather than software bugs.

brundlefly
Yeah, something's missing from the recipe or it's system-specific. I can't reproduce it, either, and I can't imagine this wouldn't have been reported before now if it were widely experienced.

Something is funky here, that's for sure. To compare X2 vs. X3, I just opened up a project in X2 with a count-in of 1, placed the NOW bar right on the loop point start, armed the audio track and hit the record button. The metronome counted off and then Sonar X2 started recording. Upon stop and inspection of the recorded audio, everything is OK and there is no delay. However, opening the same project in X3, and then performing the same test, results in the delay of audio (almost 3/4 of a bar). Now what the heck is going on here? I gotta remember what I changed in the preferences (or something) that corrects for this oddity. Hmm...
 
EDIT:  Turns out that I submitted a bug report CWBRN-18893 way back when that complained of a delay when reading an automation envelope if a metronome count-in is utilized. X2a supposedly fixed several metronome and count-in issues.

OK so I'm not the ONLY one here having this issue. I'm going to try without using the 'count-in' feature and see if I still have the same problem.