If some taxes have been configured, but have not been used in "Taxation rules" (PBA-E > Home > System > Settings > Taxation > Taxation rules), then after upgrade to 5.5.8 PBA automatically creates Tax Rules for them, so that they become effective.
/usr/local/bm/db/BM/upgrade/bm5_5_008_068/020_EUTaxAlgFix.pl creates tax rules for old taxes with non-zero rate. The issue is considered to be a software issue #PBA-60377.
For new update installations on PBA, hotfix has been released on 4/Dec/2014 (Linux) and 5/Dec/2014 (Windows). Hotfix is installed automatically during update to PBA 5.5.8.
For installations updated to PBA 5.5.8 earlier, workaround below has to be applied.
Remove incorrect tax rules from provider and all resellers (contact support if there are too many rules to be deleted manually):
PBA-E > Home > System > Settings > Taxation > Taxation rules
Use credit or debit memos to adjust affected invoices.