hiya... weird... I had this same issue not long ago... had a odd clicking noise that started at the same time I got new shoes and moved my cleats onto them... I did everything I could think of only to find out that coincidentally, the bottom bracket had begun creaking at the same time... had the LBS clean and re-lube the bottom bracket and no more creak... go figure the two things happened at the same time... Murphy's law... yep, Murphy hates me!

good luck with it...