you might have to patch HPET in your DSDT. open your dsdt in an dsdt editor and check to see if your HPET section looks like this
Device (HPET)
{
Name (_HID, EisaId ("PNP0103"))
Name (BUF0, ResourceTemplate ()
{
IRQNoFlags ()
{0}
IRQNoFlags ()
{8}
IRQNoFlags ()
{11}
IRQNoFlags ()
{15}
Memory32Fixed (ReadOnly,
0xFED00000, // Address Base
0x00000400, // Address Length
_Y10)
})
if you only see
IRQNoFlags ()
{0}
IRQNoFlags ()
{8}
add this behind it
IRQNoFlags ()
{11}
IRQNoFlags ()
{15}
recompile the DSDT save it as .aml and test it hopefully that resolves your issue.
another test would be to backup then remove System/Library/Extensions/AppleHPET.kext then rebuild your catches. you can try that before the DSDT edits to see if it really is HPET conflicting and stealing your IRQ values. if it works fine after that then replace the kext and test the DSDT edits for a permanent solution.
the problem with HPET can manifests itself as non working devices after sleep, can be USB ports, DVDROM, Wlan, Trackpad basically anything the gets designated an IRQ value.