What version of backupninja are you using? With version 0.9.3-6 on Edgy I don't seem to get that error ($SHELL is dash).
** Changed in: backupninja (Ubuntu)
Status: Unconfirmed => Needs Info
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/usr/sbin/backupninja tr: misaligned [:upper:] and/or [:lower:] construct
https://launchpad.net/bugs/60286
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