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I seem to be having the same problem :(
Upgraded from 2.4.5 to 2.5.5, things seem to work nice, except for a couple of blocks. Most of them are custom ones. If I open them for editing the content is nicely shown. Tried to duplicate them and tried to make a new one without success.
The weird thing is that I have the same problem with the "main" block, as well as "xt_themas" for theme selection.
Could you please elaborate more about "updating the theme files"?
I checked with various themes I have installed, and had the same problem. Also tried deleteing caches and they were regenerated.
Also I tried updating most of the modules, tried updating the system module again, but the problems persist.
Tried to turn on debugging mode, but most of the stuff was complaints about deprecation from some modules, not really related to this.
As far as I can see, the site is operating normally otherwise.