That sounds like a known issue. It has been resolved by "ACPI: EC: revert msleep patch". Happily Len submitted it for mainline this week. You will also find it if you try the acpi-test git tree. We're all hoping 2.6.28 will be much improved in terms of reliable operation of different ECs :).
Well, that doesn't tell us much. Did they still happen after upgrading to 2.6.28-rc3? Can we see them?
A similar bug has been reported as a regression:
<http://bugzilla.kernel.org/show_bug.cgi?id=11828>
so one assumes that it worked on the machines with linux pre-installed. Hopefully without requiring any hacks.
It seems that for now a workaround may be to pass the option debug_quirks=1 to the sdhci module...
<http://marc.info/?l=linux-kernel&m=122509648027303&w=2>
...or that it may help if you insert an SD card before booting.
Apparently the reporter also investigated pcie hotplug. Probably the BIOS doesn't provide the normal support. You can try "modprobe pciehp pciehp_force=1", maybe it helps the kernel discover the devices. It worked for something else on my EeePC. But then it will reportedly disappear the ethernet controller.
However, at the moment pciehp can cause delays of 10s of seconds during resume.
Could be this:
<http://bugzilla.kernel.org/show_bug.cgi?id=11942>
As a fix, 8fd145917fb62368a9b80db59562c20576238f5a was reverted from the acpi tree. This has also been submitted to mainline.
Thanks for your work! If you continue with this, I suggest CC'ing <kernel-testers@vger.kernel.org>. That will help Rafael the regression hunter pick it up.
Alan
--