After some trial and error and think I finally have it figured out. I was primarily using the SPDIF in, so I never really had a problem until I started using my Lemosax. When running an external pre analog into the R-44 you should run the Sensitivity (outer) at 0 and the Level (inner) all the way up. Then adjust the gain on your external pre to where you want it (on the Lemosax it was in the 11 oclock position). Make sure the limiter switch on the top is turned to OFF b/c you will not register clips accurately. My problem for weeks was that I was running the Level at about 9-10 oclock and bumping the Sensitivity up 3 clicks (10oclock), as a result, the R-44 was not registering a clip, but a brick wall. I always thought the brickwall would register as a clip, but I was wrong. If you are looking at the screen, your channels will show up on the left side of the screen as such (when running 2 x stereo):
1 L
1 R
2 L
2 R
If they start flashing during the recording, it means that you are brickwalling. This is due to the Sensitivity being turned up too high. Try turning the Sens (outer) down and the Level (inner) up. Keep in mind that is different than the Clip box that will light up when you have gone over 0. For SBD sources I start with the Level always in 12 oclock position and gradually bump up the Sensitivity until it is at the desired level.
READ PAGE 30 of the owner's manual in PDF
http://lib.roland.co.jp/manual/en/dl_08-22586/R-44_e3.pdffrom the Manual:
Adjusting the input levels
1. Turn the Input level knob [SENS] (outer) all the way left.
2. Turn the Input level knobs [LEVEL] (inner) to the center position. This position is 0 dB.
3. Hold down the [PAUSE] button and press the [REC] button.
The R-44 enters recording standby mode. During recording standby, the [REC] button blinks
and the indication alternates between REC and STANDBY.
4. Play the sound to be recorded into the microphone.
Gradually turn the Input level knob [SENS] 1 toward the right.
Sensitivity has 3 steps: Lo, Mid, and Hi.
* Sensitivity can be changed simultaneously for both MIC-L and -R with Input Level knob 1.
* When the channel name display reverses, the input level has reached the clipping level. Set the knob
to the position just before the display reverses.
5. Gradually turn the Input level knob [LEVEL] toward the right.
* Input levels of the internal mics are adjusted by Input
level knob 1 (MIC-L) and knob 2 (MIC-R).
6. Adjust the level so that the level meter shown in the
display reaches a point slightly before C (clip level).
If the recording level is too low, quiet sounds will not
be recorded. If the recording level is too high, loud
sounds will be distorted, producing a crackling noise
in the recording.
* When the channel name is blinking, clipping has
occurred at the sensitivity adjustment stage. In this case, clipping occurs even if the level meter does
not reach the clip level.
* The level meter displays the clip level (C) in values relative to 0 dBFS (FS = full scale).