RepeatMasker still did not act upon Bug 2138: Any workarounds?

We have told the guys at RepeatMasker that RM-3.1.6 have a problem
causing Bio::Tools::RepeatMasker to crash in November 2006 (Bug 2138).
And as of today, they are now at 3.2.8, and the problem is not fixed.
And I don't want my project to be stalled-- any tips for a workaround?
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