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I have just replaced the power supply and motherboard in my PC, the motherboard is the same model an Asus P7P55D-E LX and the power supply is an Antec TruePower New 650W Modular PSU

prior to the replacements my PC would go to shutdown automatically or manually without an issue, now with the same installation of Windows 7 when the computer goes into standby as windows seems to be going to sleep the entire box powers down, when its restarted I get a message about windows not shutting down properly.

Any Ideas?

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Check that any ACPI settings in the BIOS are the same as for the old motherboard. If you can't remember, note down the current setting/s and try some different ones.

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You also might want to check out your power management settings and play around with them to see if there's anything differently that happens once you do switch them. You may also find this of some help:

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