Did you already check the interrupt priorities?
Can you please post your complete project, so that we all can have a look at all of your settings. To do so, use
Creator->File->Create Workspace Bundle (minimal)
and attach the resulting file.
All your interrupts have got the same (lowest) priority.
In .cydwr view under "Interrupt" tab you may change the priorities from 7 (default, lowest) to other values.
Avoid to use priority 0 (highest).
I would try
RTC prio 7
SD prio 5
all others prio 6
Didn't solve the issue. I tried other priorities also with no luck.