Thoes updates can't do that (or shouldn't), probably the kext cache was cleaned and rebuild incorrectly, perhaps you are suffering from a kext corruption but as it was booting from the cache you never noticed that problem. Just some ideas you may check.

To rebuild caches you can use your install disk and delete extensions.mkext or insert -f into darwin's prompt. You may also try restoring iousbmassstorageclass and iousbfamily kexts.

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CPU: AMD Athlon 64 3000+ @2.3Ghz - Motherboard: ASUS A8N-SLI nForce4 SLI - nForceLAN by eno - SuperNForceATA by Medevil - RAM:2 GB DDR 333Mhz Audio: ALC850 Video: XFX nVidia GeForce 8400GS 256Mb (0x06e4) QE & CI from Chameleon 2 RC4Ethernet: Realtek RTL 8139 Series (working out of the box) OS: Snow Leopard 10.6.4 (aryajuanda's guide) + Windows XP 64bits