Somebody was paying attention. Yellow jumper was some test during development. :)
Thermal paste is irrelevant, as for initial functionality tests CPU is not even overclocked. This was one of the first boards for R&D team to work on. 
 
Colored marks on chipies means that chipie was programmed with some firmware. Different color = different firmware. Just means to identify what board has what when it came from factory with naked eye, instead of connecting development programmers to read the version, etc. 
 
What other changes can you spot? :P