Plugin saves configuration to
~/.config/xfce4/panel/XfceTimer.rc and loads it from there
instead of per-instance rc files
~/.config/xfce4/panel/xfce4-timer-plugin-ID.rc. This causes configuration of all but one plugin instance to be lost on restart. This has been fixed.
To be honest I don't know the reason for panel rc configuration bypass with
XfceTimer.rc. Source does not mention it. I'm guessing that there could have been some problem with rc file handling in the past which has been resolved in the meantime. For me everything works correctly now.