The issue is gone now when I tried again with tracing over USB. I just came across another issue though: the MCU lost connection over I2C to the modem, and no matter what the MCU did / restarting etc, nothing happend. Just could not get any response from the notecard (i2c NAK). I could not see anything in the trace output (not sure when it happened), but the notecard looked like it was doing its thing, trying to get a GPS fix and occasionally connecting.
Resetting the modem fixed the issue immediately.
Edit, seems to have happened again, trace:
G17:30:15.73 GPS search (21 sec, 33/33 dB SNR, 0/6 sats, HDOP 0)
R17:30:19.19 bulk: created file:data/axl-qo.001
G17:30:20.73 GPS search (26 sec, 33/34 dB SNR, 0/4 sats, HDOP 0)
G17:30:25.73 GPS search (31 sec, 34/34 dB SNR, 0/4 sats, HDOP 0)
G17:30:30.73 GPS search (36 sec, 33/34 dB SNR, 0/7 sats, HDOP 0)
G17:30:35.73 GPS search (41 sec, 34/34 dB SNR, 0/7 sats, HDOP 0)
G17:30:40.73 GPS search (46 sec, 34/35 dB SNR, 0/7 sats, HDOP 0)
G17:30:45.73 GPS search (51 sec, 34/35 dB SNR, 0/8 sats, HDOP 0)
G17:30:50.74 GPS search (56 sec, 36/36 dB SNR, 0/8 sats, HDOP 0)
G17:30:55.73 GPS search (61 sec, 36/36 dB SNR, 0/7 sats, HDOP 0)
R17:30:59.05 bulk: created file:data/axl-qo.002
G17:31:00.74 GPS search (66 sec, 34/36 dB SNR, 0/9 sats, HDOP 0)
G17:31:05.74 GPS search (71 sec, 36/37 dB SNR, 0/9 sats, HDOP 0)
G17:31:10.74 GPS search (76 sec, 37/37 dB SNR, 0/9 sats, HDOP 0)
G17:31:15.74 GPS search (81 sec, 36/37 dB SNR, 0/9 sats, HDOP 0)
G17:31:20.74 GPS search (86 sec, 36/37 dB SNR, 0/9 sats, HDOP 0)
G17:31:25.74 GPS search (91 sec, 36/37 dB SNR, 0/9 sats, HDOP 0)
G17:31:30.74 GPS search (96 sec, 36/37 dB SNR, 0/9 sats, HDOP 0)
G17:31:36.74 GPS search (102 sec, 37/37 dB SNR, 0/9 sats, HDOP 0)
R17:31:38.82 bulk: created file:data/axl-qo.003
G17:31:41.74 GPS search (107 sec, 37/37 dB SNR, 0/9 sats, HDOP 0)
G17:31:46.74 GPS search (112 sec, 35/37 dB SNR, 0/9 sats, HDOP 0)
G17:31:51.74 GPS search (117 sec, 37/37 dB SNR, 0/8 sats, HDOP 0)
G17:31:56.74 GPS search (122 sec, 37/37 dB SNR, 0/8 sats, HDOP 0)
G17:32:01.74 GPS search (127 sec, 37/37 dB SNR, 0/10 sats, HDOP 0)
G17:32:06.74 GPS search (132 sec, 36/37 dB SNR, 0/9 sats, HDOP 0)
G17:32:11.74 GPS search (137 sec, 36/37 dB SNR, 0/9 sats, HDOP 0)
G17:32:16.74 GPS search (142 sec, 35/37 dB SNR, 0/9 sats, HDOP 0)
R17:32:18.86 bulk: created file:data/axl-qo.004
G17:32:22.74 GPS search (148 sec, 34/37 dB SNR, 0/5 sats, HDOP 0)
G17:32:27.74 GPS search (153 sec, 36/37 dB SNR, 0/8 sats, HDOP 0)
G17:32:32.74 GPS search (158 sec, 35/37 dB SNR, 0/8 sats, HDOP 0)
G17:32:37.74 GPS search (163 sec, 36/37 dB SNR, 0/8 sats, HDOP 0)
G17:32:42.74 GPS search (168 sec, 35/37 dB SNR, 0/8 sats, HDOP 0)
G17:32:47.74 GPS search (173 sec, 36/37 dB SNR, 0/8 sats, HDOP 0)
G17:32:52.74 GPS search (178 sec, 35/37 dB SNR, 0/8 sats, HDOP 0)
G17:32:57.74 GPS search (183 sec, 35/37 dB SNR, 0/5 sats, HDOP 0)
R17:32:59.62 bulk: created file:data/axl-qo.005
G17:33:02.74 GPS search (188 sec, 35/37 dB SNR, 0/7 sats, HDOP 0)
G17:33:07.74 GPS search (193 sec, 34/37 dB SNR, 0/7 sats, HDOP 0)
G17:33:12.74 GPS search (198 sec, 30/37 dB SNR, 0/6 sats, HDOP 0)
G17:33:17.74 GPS search (203 sec, 33/37 dB SNR, 0/6 sats, HDOP 0)
G17:33:22.75 GPS search (208 sec, 32/37 dB SNR, 0/12 sats, HDOP 0)
G17:33:27.75 GPS search (213 sec, 32/37 dB SNR, 0/12 sats, HDOP 0)
G17:33:32.75 GPS search (218 sec, 32/37 dB SNR, 0/13 sats, HDOP 0)
G17:33:37.75 GPS search (223 sec, 32/37 dB SNR, 0/13 sats, HDOP 0)
G17:33:42.75 GPS search (228 sec, 32/37 dB SNR, 0/9 sats, HDOP 0)
G17:33:48.73 GPS search (234 sec, 33/37 dB SNR, 0/15 sats, HDOP 0)
G17:33:54.73 GPS search (240 sec, 33/37 dB SNR, 0/15 sats, HDOP 0)
G17:33:59.74 GPS search (245 sec, 28/37 dB SNR, 0/5 sats, HDOP 0)
G17:34:04.74 GPS search (250 sec, 30/37 dB SNR, 0/11 sats, HDOP 0)
G17:34:10.74 GPS search (256 sec, 28/37 dB SNR, 0/12 sats, HDOP 0)
G17:34:16.73 GPS search (262 sec, 28/37 dB SNR, 0/12 sats, HDOP 0)
G17:34:22.73 GPS search (268 sec, 28/37 dB SNR, 0/12 sats, HDOP 0)
G17:34:27.73 GPS search (273 sec, 29/37 dB SNR, 0/6 sats, HDOP 0)
G17:34:32.74 GPS search (278 sec, 29/37 dB SNR, 0/8 sats, HDOP 0)
G17:34:37.75 GPS search (283 sec, 28/37 dB SNR, 0/9 sats, HDOP 0)
a reset fixed it (pushing the reset button on sparkfun carrier board).