@pghaworth: If you put the packages in the root folder, fw 5.6.1 will wipe them mercilessly, as you experienced

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On the other hand, if you want to use MR Installer [which you kind of have to, right now, on FW >= 5.6.1 ^^], put them in the mrpackages folder (and, hopefully, that should keep them safe from the FW).
Note that, when you ran MR Installer with an empty mrpackages folder, you should have seen a "No MR Packages found" printed at the bottom of your screen...
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And of course: many thanks for taking the plunge

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