How are you viewing the images? I've never had a problem with losing the time taken tag from Exif. It is there as an option in Bridge, and works fine regardless of file type. In Windows 7, the date created column was not visible by default for me, but right clicking any column heading gives the option to turn it on, after which you can sort by that column.
In Photoshop we are converting/color adjusting and saving raw files to psd and it is changing the date created and date modified to the time the image is saved. This is a huge problem as we have to merge multiple photographer files into a single timeline. We are working in Mac OSX.
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I just tried it again, and even saving under a new name maintains the correct 'Date time taken' tag in EXIF
I think you are confusing the capture date of the image, which is stored by the camera in the Exif metadata in the image, with the creation/modified dates that your OS uses to keep track of its files. If you use sort by capture date in Photoshop or Lightroom, it will used the original capture date in Exif. If you sort by file creation date in your OS browser, it will usually use the file creation date, not the image capture date.