Alfred syncs the relative position of its window across machines.
I think this is a bad idea. I have a monster 30" display on my desktop machine (where it's easy to miss things), but an 11" MacBook Air.
On my desktop, I like Alfred to appear roughly in the centre of the display where I'm looking, but on the MBA it has to be near to the top of the screen or the full results list doesn't fit on the screen.
While it's not a huge deal to have Alfred's window appear near the top of my 30" screen (once I realised what was going on—for a long time I thought Alfred had crashed), it strikes me as much more logical for window positioning (and size, where relevant) to be machine-specific rather than user-specific.
I found it particularly confusing, as my theme was not synced (it wasn't installed on the MBA).