After occurring for everyone but me in a ctf game, I realised the cause for flags/bombs not to appear occasionally on maps.
If someone edits their map and moves the base locations, and then plays that map online. The bases are positioned by the server for whoever joins the game first (or loads the map first), at least it seems that way.
For everyone else, the bases (and flags/bombs) are still missing and can't be interacted with.
If the person who modified his bases comes later on, he can still see the flags/bombs as normal though.
This is pretty easy to reproduce on a server by using a modified map, starting the game, then renaming the maps and launching another client and connecting to the server. If you then 'reset' and try it the other way around, you'll see bases/affinities normally.
Tested in r6550, although it seems to effect 1.4 players too, so it'd probably also an issue 6550+.