Hi Scott,
Well I can confirm that the problem is that there are two service packs... one for Quartus, and one for Nios. They are separate installs, and the Nios service pack is what has the extra delay fix... I went through *everything* to fix all instances of that, including ASMI.
This is a bit of an anomaly as we have been working to sychronize with the Quartus release for several products, including Nios.. and indeed the "major" (twice-yearly non-service-pack) releasees should all ship concurrently now. However, this SP was an exception. Apologies for any confusion this has created.
About the problem itself:
There should really be, at most, three things to do to fix this manually (no service pack):
1. All instances of 'extradelay' in the .pm file in the asmi component
2. the class.ptf file in the asmi component
3. After the changes are made, open sopc builder, remove all ASMIs in your system, and add them back. This should refresh the system PTF file.