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matt:
There is a bit of the chipKIT core which embeds some pointless information into your compiled sketch. I disagree with it since it often breaks things. One of the things in there is the version of MPIDE that was used to compile the sketch. Since MPIDE no longer exists it's irrelevant. I have been campaigning for ages to have that chunk of data removed.
The linker script has a test that confirms if the information block is the right size. If it's not it throws that cryptic error. But since the only thing that's specified from outside the linker script is the MPIDE version it's kind of logical I guess.
The actual value is stored in a variable in one of the core source files. If that is being optimized out incorrectly, or that file not being compiled, it can throw a wobbly. Most times this is because compilation failed but it thinks it worked, so doesn't try to compile again. Most problems like this can be cured by doing a "clean" build - hold the SHIFT
key while clicking the compile button - it deletes any cached compiled files and builds everything afresh. Takes a little longer to compile, but forces it to try and work again.