pt-online-schema-change

I am using the tool to rebuild a table while compressing it.
The remaining time gets up to 99% 00:00 but it is still going for a long time.
I am looking at the process list and see that it is not even half way though data (going by PK ID).
Amy ideas why the progress/remain time is way off.

Variable_name,Value
innodb_version,5.6.28-76.1
protocol_version,10
slave_type_conversions,
version,5.6.28-76.1-log
version_comment,Percona Server (GPL), Release 76.1, Revision 5759e76
version_compile_machine,x86_64
version_compile_os,Linux