Update: I followed the video requirements posted in this forum, and it seems to have fixed the majority of the synching issues.
Basically, that the video cannot be larger than 320w x 240h, no anamorphic, mpeg4 ffmpeg codec, 29.97 constant framerate, avg bitrate of 1000 kbps, aac (faac) stereo with 44.1 samplerate and 128 bitrate. I also try to cut videos into pieces that are no longer than 1 hour each (most are around 42-46 minutes).
However, I still have some files that just are not read in the Sansa. I have had a lot of trouble with micro SD cards lately, and that happened after the latest firmware update. I did not have trouble before that. I cannot use the Sansa encoder because it fails every time and errors that it cannot write to the device. So, the synching is fixed by using Handbrake and the above settings.
Thanks, halonachos117 for the tip. I will keep trying!
