rParker is having a similar problem on this forum. I wonder what the "common factors" are between you problems and hardware designs?
Here's some more complications concerning VSTBY and the RTC:
Current Consumption - higher than you might like if you're using a "button cell":
https://community.freescale.com/message/51910#51910
If you have a battery on VSTBY and it goes flat, it seems the RTC won't run, so you probably do need to run VSTBY from a diode from the battery and a diode from 3V3 (which would fix your current 3.6V battery problem).
https://community.freescale.com/message/82160#82160
> If VSTBY is greater than VDD it doesn't boot.
Do you mean by a particular amount, or does it fail at say 3.301V? there usually has to be a difference enough to forward-bias a junction for it to have an effect.
The Data Sheet apparently gives a maximum voltage for VSTBY of 3.5V, so that looks like "0.2V above 3.3V". So if your 3.3V is within spec but LOW and your battery is within spec but HIGH... If this is the problem then the spec for VSTBY should probably be "VDD+0.2V".
There's a very interesting section in the Data Sheet:
RAM standby supply current
* Normal operation: VDD > VSTBY - 0.3 V = 5uA
* Standby operation: VDD < VSS + 0.5 V = 20uA
So there's logic that switches at those relative voltages - or they're the minimum and maximum comparison voltages. The MCF52110 is quite different - check its specs for the strange "transient" operation.
I suggest you download all Reference, Data Sheet and Errata for every part that has a VSTBY pin (52259, 52110, 5213, 52223, 5282, 5301x) and see if some of the manuals tell you something interesting the others don't.
What is the timing relationship between your 3.3V turning on and the external reset signal going away (assuming you have an external reset controller)? If the Reset is going away before the 3.3V is fully established, then the problem might be the difference between VSTBY and VDD at that point. It may be related to when the crystal starts oscillating relative to the 3l3V ramp and the Reset signal.
Tom