I am looking at flights YYJ -> RSW (Fort Meyers) for Feb 2013, specifcally the 4th, but it is happening on multiple days I've checked. Booking for 3 px, in case it matters.

Flight option 1
AC190 - Upgrade available
AC1234 - Upgrade available

Option 2
AC190 - Upgrade NOT available
AC1236 - Upgrade NOT available

Option 3
AC190 - Upgrade NOT available
AC1232 - Upgrade NOT available

Option 4
AC8050 - Upgrade not available
AC116 - Upgrade Available
AC1236 - Upgrade Available
...

AC190 is sometimes availale sometimes not, AC1236 is sometimes available, sometimes not.
I can't post a screencap to show it, but it is very weird. Thinking about purchasing Latitude to upgrade, but I am not confident that the upgrades will succeed with these flakey results.
Anyone else experience this?

Hmmm, obviously the legs that have both upgrade space available now will both be blue boxes, but I see your point about AC190 not having upgrade space available when show with AC1236, and that is a bit strange. And if you really want AC190 and AC 1236 just call in and book that flight, no charge to call and book. But AC8050 is Jazz so no J on that flight. But if you book Latitude you will have instant confirmation to J on option 1 - if you don't get all of your upgrades immediately easy to cancel within 24hrs for free either on line or via phone.

What are the options?

I always cross-check with KVS.

That may not help when trying to confirm an upgrade though?

I trust ac.com blue square less than I trust KVS or other tools that directly show R inventory.

Since you're planning to buy a B fare anyway, if ac.com won't confirm the upgrade due to IT failure, you can call in and have the agent do it. If they won't do it for whatever reason, you cancel and get your money back!

I have yet to have to a problem when I have checked with KVS and then bought ticket and upgraded immediately, including a few R=1's. I cannot say the same for the AC website, as in the early days I was put off by the inconsistent fare display when asking for upgradable options. I am now used to using KVS and that's what I do.

Why not try booking two one ways?

^

i have seen this before as well on bookings from Canada to the USA - especially when there are multiple options on the Canadian segments to the hubs.

US flights don't seem to have the buggy IT issues in my experience.