It strikes me that either Jack/Ianto really isn't that important to the show (or all of the writers would at least be on board enough to write it with some relative consistency) or there is deep division in the writing staff about the relationship (and therefore some of the writers choose to subvert or ignore it).

I recall the writing on BtVS for Buffy/Spike taking on very different characteristics depending on whether the writer in question supported the relationship.