If I got paid every time some part of Debian confused someone when installing weathermap, I'd have enough money by now to work on the thing full time. I feel like I must have spent a couple of working days in the last 6 weeks going around and around 2 issues in Debian, neither of which I have any control over, and neither of which are actually weathermap problems.
1) There are two PHPs. They are different. They have different config files.
2) GD is borken in the current 'stable'.
Finally 3) check.php was intended to help with the basic checks, not to mean that if it says OK, then there are no possible problems. Maybe that was a mistake. But last time I put a message in something to say there might be a possible problem, it was interpreted as an error message, so that's a mistake too.
Err, rant over.