Ok, I think we are getting closer to what's going on. It looks to me like our good friend joe (jwm) is mis-calculating the width required for the combination of the clock and tracker. It has something to do with restarting the process causing tracker to restart and display "starting" . The clock and swallow width are set for "starting" and clock, and don't adapt correctly when "starting" changes to the tracker status output format. The fix for me is to set the clock width to 75 ( I assume is in pixels). I tried this setting for both 1024 and 1400 screen densities and it worked for both. However, I suspect it is affected by screen size so perhaps 1900 x1080 for instance may need a different number for clock width.
So the fix is to add width=75 in the <Clock> ... line in ".jwmrc-tray".
Edit: By the way I did try to set the width of the swallow window but this does not fix the problem. The Clock width must be of a fixed width to fix the problem.