I linked this recently (36 days ago)
According to Jarrod's comment on this post, linked accounts should get 100 rep if any of the others have more than 200. Looks like I hit a bug or something, I got the 100 rep points on meta and SF.
Not that I'm bothered about the rep, but I feel it is my duty to report such issues immediately should I encounter one. *salutes*
Daniel's answer is a suitable workaround. I can't help wondering if I should have left it as is until the bug had been investigated, though.
ire_and_curses pointed out that this bug is probably no longer relevant due to the auto-linking feature introduced today.