I have an open SR and DR on a similar (maybe the same) issue. Rules do not port correctly from PADS Logic to PADS Layout; DRC checks don't catch the violations. The SR has been open since May 2014. The problem was shelved and then reopened in June 2015, and I have had no update since then. You should submit an SR for this.
I have come across this issue again in another design and looked deeper into it. It seems random nets are being grouped together in temporary netlist files that are generated during the eco.
The two files in question are:
In these files I see a "rule set" where one or more (random) nets have been grouped together to use the same rule. In Logic, the rules for these nets are different and there are no other "conditional" or "class" rules. Somewhere, these two nets have been logically linked in some manner and this seems to cause the Eco errors. I do not know what generates the two aforementioned files but even if I delete the affected nets and recreate them the same nets are re-linked together (even though they have different names). Is there any setting that can link or group nets together or is a bug just generating incorrect rule information?