I found a workaround for the problem. Enabling the "USB S3 Wake-Up" BIOS option seems to fix this problem. I had it turned off since I bought the machine, but I guess something was introduced in 3.9 that triggers the issue. Judging from the amount of ACPI related issues on Samsung laptops, a true solution for the problem would be to never install Linux on them.
I found a workaround for the problem. Enabling the "USB S3 Wake-Up" BIOS option seems to fix this problem. I had it turned off since I bought the machine, but I guess something was introduced in 3.9 that triggers the issue. Judging from the amount of ACPI related issues on Samsung laptops, a true solution for the problem would be to never install Linux on them.