Perhaps, the timing out is something like this :
https://www.mobileread.com/forums/showthread.php?t=66170
I was having problems too with checking forums and doing other things and getting the UART clk gated message from short inactivity period.
I simply commented out the lines related to that particular "if" check in the /etc/init.d/power file (leaving only
echo 0 > /sys/devices/platform/mxcintuart.0/uart_clk_state
as I could not write to /mnt/us directory (kept getting NFS stale there).
This is not optimal but now I do not have to worry serial going to sleep.