We had a little argument about how alignment was counted. The wording says:
"If they have five more abilities associated with one particular deity than they have any of the other Chaos gods…"
Cymbel has the right of it.
The sentence structure seems equal parts goofy grammar and conservation of page space. You have paraphrased the rule, and that may or may not have contributed to your misunderstanding of it. Had it read as follows:
"…(by having five or more advancements that are dedicated to any one Chaos Power than are dedicated to any of the other Chaos Powers)…"
it might be more clearly understood.
This particular rules question may be answered by checking pg 75 of the Black Crusade Core Rules, the section titled Checking Alignment. Note: A PC does not automatically become aligned to a Chaos Power simply because he has five (or more) advancements dedicated to any one Chaos Power than he has dedicated to any of the other Chaos Powers. Alignment does not change as a result of purchasing advancements. He must reach a Corruption Threshold (10, 20, 30, 40, and so on). Each time a PC reaches a Corruption Threshold the Player then must compare the number of all dedicated advancements, and if the PC meets the "requirement of five" his Alignment changes.
Additionally, the GM may (at his/her discretion) consider changing Alignment form one Chaos Power to another (or to Unaligned) as being a lesser Failing, earning the PC d5 Corruption Points (see pg 290 of the Black Crusade Core Rules, the section titled THE PRICE OF FAILURE for more details).