JB,
Is your customer running 2.0 or 2.0R1? Your customer should be running 2.0R1, it fixes a bunch of bugs in the product.
I received an email from a member of the SMMOSS product team regarding this behavior you describe.
He told me that SMMOSS is designed to pause the MOSS index activity, backup the MOSS index, and then resume the MOSS index activity.
I have always told my customers to try their schedule their backups around the MOSS crawl, so I never hit my head on this.
It is recommended that you open a case with NGS or file a BURT.
Thanks,
Mark