I have experienced the same problem; it happens sometimes when copying and pasting blocks, that the flow logic is damaged. Look to see if the LEGO pieces that you put the blocks on is not continuous. It is a serious problem with the software that needs a fix. As it is, I do not recommend copying and pasting more than a block at a time. Keep lots of versions of your program so you can revert to an older saved version if you corrupt your file. If you do not have an older version, you may be forced to rewrite your program completely
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Try seeing in your NXT 2.1 software shows some more grayish looking blocks then delete them then replace them, if that doesn't work then save the orignal code then create a new tab, after that you Restart your code and switch tabs to take a look and if that doesn't fix it then try new sources. By, D3 Studios, We make better.