Where is the data stored and how is it accessed by the two processes involved?
If the structure was allocated off the heap, try allocating a much larger block and putting large guard areas before and after the structure. This should give you an idea of whether it is one of the surrounding heap allocations which has overrun into the same allocation as your structure. If you find that the memory surrounding your structure is untouched, and only the structure itself is corrupted then this indicates that the corruption is being caused by something which has some knowledge of your structure's location rather than a random memory stomp.
If the structure is in a data section, check your linker map output to determine what other data exists in the vicinity of your structure. Check whether those have also been corrupted, introduce guard areas, and check whether the problem follows the structure if you force it to move to a different location. Again this indicates whether the corruption is caused by something with knowledge of your structure's location.
You can also test this by switching data from the heap into a data section or visa versa.
If you find that the structure is no longer corrupted after moving it elsewhere or introducing guard areas, you should check the linker map or track the heap to determine what other data is in the vicinity, and check accesses to those areas for buffer overflows.
You may find, though, that the problem does follow the structure wherever it is located. If this is the case then audit all of the code surrounding references to the structure. Check the contents before and after every access.
To check whether the corruption is being caused by another process or interrupt handler, add hooks to each task switch and before and after each ISR is called. The hook should check whether the contents have been corrupted. If they have, you will be able to identify which process or ISR was responsible.
If the structure is ever read onto a local process stack, try increasing the process stack and check that no array overruns etc have occurred. Even if not read onto the stack, it's likely that you will have a pointer to it on the stack at some point. Check all sub-functions called in the vicinity for stack issues or similar that could result in the pointer being used erroneously by unrelated blocks of code.
Also consider whether the compiler or RTOS may be at fault. Try turning off compiler optimisation, and failing that inspect the code generated. Similarly consider whether it could be due to a faulty context switch in your proprietary RTOS.
Finally, if you are sharing the memory with another hardware device or CPU and you have data cache enabled, make sure you take care of this through using uncached accesses or similar strategies.