Hi there,
It seems, that I had the same problem. AFAIK fix_table and hbck
currently won't be able to fix this, so I wrote myself two small
tools.
A first one detects such loops in the meta table:
https://gist.github.com/894031#file_h_base_region_loops.java
If you specify '--fix', the loopy/duplicated regions are moved to a
directory you specify and the meta is updated.
The second one 
(https://gist.github.com/894031#file_add_records_from_region.java)
takes one of a moved region as input and adds its content to the
specified table, if there isn't already an entry with the same
family:qualifier (this fitted my needs, as I only have one entry per
family:qualifier).
DISCLAIMER: Those tools were programmed rather quickly, so please make
sure, that they serve your needs.

If you have fixed your table, I would migrate as quickly as possible to 0.90.x!

Best,
Lukas

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