I have some ideas, but could be poking around in the dark without enough information. I'm a bit foggy on IOD generating symbols but not using symbol generator. Using generic symbols sounds like you are using the schematic update design process. I have a cheat sheet that describes one way to design from choosing a part all the way through layout so you can clearly see what IOD does for you in this design flow. Feel free to contact me to figure out how you want to use IOD. If it includes using the IOD symbol generator, the confusing properties should get cleaned up when a new symbol set is written.
I was basically just trying to use IOD to speed up the symbol generating process, as opposed to "starting from scratch" like I would do for smaller parts. It was just a way to get all the pins/pin names onto symbols, and IOD makes it pretty easy to filter based on bank number, Vcc, etc. Probably not going to use IOD for this device after this. Once the symbols were exported, I am using symbol editor to go in and clean up things a bit. It was then that I noticed the "weirdness". I'm starting to spend some time "hand-editing" for clean-up, so at some point, it's going to get to the point of not worth the effort to re-generate from IOD, because then I have to start my cleanup all over again. As I'm checking the pin names against the Altera pin-list, I see a lot of pin labels that aren't complete as far as second and third functions. At some point in the process, while trying to update the IOD parts, it told me it couldn't update unless the version of IOD was updated, but I can't do that until we're ready for everyone who uses Dx/Expedition is ready to update. We're still waiting to jump to xDxDesigner/Xpedition until we run at least one pilot design through. It might just be that this part is new enough that I just can't use IOD for it, until we've made that move. Not sure what to think at this point, but I think I'm done with IOD for now, too much time wasted already.
OK. Sorry about the wasted time. Next time you are playing in this sandbox, give me a ring and we could maybe share a webex to clear things up.