Well, some filters slightly change the size of the objects (on which they are applied) and it could cause unusual alignment since it visually may look incorrect. Alignment relies on object absolute size, depicted by the bounding box, and it`s not always where you think it is.
Here`s an example...
A4 page / bellow is the text without the effect

...and how does it looks when selected in Inkscape

Filters uses a matrix to produce the effect and that`s why the effect looks different on different parts of the document (since you may change it`s position and size relative to the page, kind of a mask or tiling - so to say). Open your .svg with the "pate d`or" and go to Filters/Filter Editor. There you`ll find a new playground ,)
p.s.
And, yes... moving the object involves recalculating of the effect, which may cause the incorrect rendering. Not sure if it`s a bug or not. Personally, I don`t use filters that much.