Sorry about that, you should have a PM now.
1. That makes sense. I looked, and I do need to fix it to remember your choice for the next beta.
2. That does sound like it could be with our environment handling. Looking at it, I see that there are some places where I could miss that a project needed the tasks to be upgraded from a previous version, so this may be a combination of the two problems.
3. In general, if you open a project, you should see any other tags in any other projects. The tags from the sub-projects go either to the workspace tag file, or a project specific tag file - but in both cases those tag files are searched from no matter with sub-project you have active. So if you're not seeing tags from a particular project, my primary concern is that the files for that project aren't being registered in the tag file. Back to gradle specific details, that might happen if the sub-project wasn't generated correctly, and is accidentally excluding the project's source files.
In the project view, if you expand a sub-project, and it doesn't show any source, that's a definite problem. If it does show source, something else is going on, the other debug information you're gathering will narrow down what's going on there.