Hi Joan,
We also ran into a similar issue during reboot tests in a relatively low probability (around 1% of reboots). We have this issue on various screen resolutions, 640*480, 1366*768, 1280*720, seems not related to the 1024 pixel limit.
We have the following logs:
Linux version 3.14.28+g35438a2 (autobuild@optbuild3) (gcc version 4.9.1 (GCC) ) #1 SMP PREEMPT Fri Jul 3 09:28:14 NZST 2020
...
imx-ipuv3 2400000.ipu: IPU DMFC NORMAL mode: 1(0~1), 5B(4,5), 5F(6,7)
imx-ipuv3 2800000.ipu: IPU DMFC NORMAL mode: 1(0~1), 5B(4,5), 5F(6,7)
...
platform ldb.13: Driver ldb requests probe deferral
platform fb.27: Driver mxc_sdc_fb requests probe deferral
platform fb.28: Driver mxc_sdc_fb requests probe deferral
platform ldb.13: Driver ldb requests probe deferral
platform fb.27: Driver mxc_sdc_fb requests probe deferral
platform fb.28: Driver mxc_sdc_fb requests probe deferral
...
mxc_sdc_fb fb.27: registered mxc display driver ldb
imx-ipuv3 2800000.ipu: IPU DMFC DP HIGH RESOLUTION: 1(0,1), 5B(2~5), 5F(6,7)
mxc_sdc_fb fb.28: registered mxc display driver ldb
mxc_sdc_fb fb.27: timeout when waiting for flip irq
...
I also used an oscilloscope to capture LVDS ouput clock, with disabled video config in u-boot to get rid of unnecessary clock waveform, we have the following results:
This is the working one:

This is the failing one:

I also dumped all IPU, CCM, CCM Analog related registers when this issue happened, here're the registers compare (after we have the "timeout flip irq" kernel message):

And further investigation shows 0x02a40174 is the first register which could tell this issue is happening, there's a "DI1_CNTR_FIFO_EMPTY" flag got cleared in this register.
I've been looking into this for a short while, before your recent reply on this post. I've already tried "dmfc=3" argument in kernel command line and the patch. They turned out to be not helpful on this issue.
Could the information I provided above be able to concluded as we are running into the same issue you're discussing? Looking forward to hear from you. Thank you very much.
Kind regards,
Max