I've played with it some, but it remains confusing. Transfix is now working right, though I didn't change anything. I did find that the spells work just fine if I prep them unmodified; the error only shows up when I go to attach a metamagic feat. But every spell I create now has the issue, though it's only the most recently created spell, which leads to the first workaround I've found.
I ran the timing reports for both portfolios, and they don't seem to relate in any way to those portfolios. I don't have any idea what the report is supposed to be. It's just a long, long list of pretty much every ability available in Hero Lab. Looking through the forum, I found something that says that the only thing that really matters is the stuff at the very top, but that doesn't actually help here, since what it says at the top is:
<document game="Pathfinder Roleplaying Game">
<unknowns> </unknowns>
<duplicates> </duplicates>
<errors> </errors>
so it doesn't help at all.
I tried my first idea for a work around by creating a new spell,
dummy spell, which has nothing at all in it. At first, this didn't help. So, I started adding tags one at a time. It turned out that the cause of all of this is when I add a Source for the spell. After compiling with just that change from the last version, the error message showed up in
dummy spell, and the second to last spell I'd created worked right.
So, it seems like there is a conflict between the metamagic system and Sources. That doesn't make any sense to me, especially since it only applies to the most recently created spell.
I don't know if any of that helps or is useful, but I thought that I would report it.