By 1" square I take it you mean the Nielsen N97 aluminium profile?
News Flash - something I have long known and my suppliers have long denied is that different batches of this moulding will not line up properly when you join them. The thickness seems to vary so that you will get an untidy step of up to a millimetre in the corners.
The only solution I have come up with is to mark or scratch a date on the back of all the offcuts so I can match them up when using them. Sometimes the ribbed markings in the channel at the back can be used as a guide to compatibility but, usually, I test join all offcuts before cutting them. It is a P.I.T.A. but this stuff is too expensive to waste and too useful to give up.