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In short: there is no problem here.
You do not convert the CR2 file to DNG version 4.6 or 5.4; these numbers relate to the program version of the DNG converter.
You need the newer version of the converter, because the former versions do not "know" the 500D. When converting the 500D CR2 with the new DNG converter, you can choose the DNG format version 1.1 or 1.3 on the "Change preferences" subdialog; however, no matter what you select, the output will be compatible with 1.1, which is supported by ACR in CS2 (perhaps in CS1 as well?). This is so, because the 500D does not offer any functions, which are not covered by the older DNG format but are covered by the newer version.
I'm not using Adobe DNG Converter. I convert CR2's to DNG in Lightroom 2 when importing photos from memory card.
In Lightroom (2.4) preferences there's an option to choose:
In that pull-down menu there's several options:
I'd understand if there was versions 1.3 and 1.2 to choose, but not. So you say that, if I convert to 5.4 (in that previous pull-down menu) the dng-file created will be compatible to Photoshop CS3?
Maybe I need to test this...
If I convert CR2 to DNG using Adobe DNG Converter, it'll say "compatible with Camera Raw 5.4 and later". Still it seems that my Photoshop CS3 will open DNG-file, even if there's only Camera Raw 4.6 installed/supported.
1. I am not using LR, but I think LR uses almost the same DNG converter code with a different UI.
2. The options 1.1 and 1.3 appear under "custom".
3. Again: the 500D DNG does not have any DNG version dependency above 1.1. No matter, which version you select, you get the same result, and that will be accepted by ACR of your Photoshop.