This is a recurring question for which I give you my recurring answer:
I had a similar problem and first tried to convert my data as well. But, than noticed my Geotiff had a compression applied ('PACKBITS'). After exporting my dataset (right click layer =>Export Data) to an uncompressed Tiff (Compression type: NONE), the problem was solved: NoData cells behave again like expected and you can carry out again common NoData operations. So have a look at your layer properties to see if your Tiff has been compressed as well and if so uncompress it.
Good luck and best wishes,
Alfred Wagtendonk
Have you tried the resample datamanagement tool?http://resources.arcgis.com/en/help/main/10.1/index.html#//00170000009t000000
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