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The reason is that JBPatch 4.0.0 (and the patches) are essentially incompatible with previous versions/patches - which is indicated in the system log (old patches are ignored). But it might leave people wondering ("but... the files are there, so why don't the patches show up?") - and to prevent this, I recommend a clean reinstall.
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I was on firmware 5.3.1 and JBPatch 3.2.1, I first updated to firmware 5.3.4, then tried to clean JBPatch with uninstall.bin from 3.2.1 but it failed with an error message, something like 'uninstall failed'. After that I installed new JBPatch 4.0 and Kindlet Jailbreak and all works fine. When I start JBPatch 4.0 now, the margin patch shows up in the patchlist and it is greyed out. Is there a chance to get rid of it?