When you have problems where a machine only has problems booting when cold, the culprit is almost always hardware. First, it may be hard drive related. As a drive ages, the lubrication used on the bearings starts to thicken. When the drive is cold, the thickened grease can prevent the drive from spinning up in time. Usually, the boot process doesn't get as far as Windows though. As the grease warms, the drive is now able to spin more freely and will work fine.
Also, when cold, metal contracts. This may cause bad connections of your memory, cpu and cables. You can try removing and reseating your memory, cables and expansion cards. It could be that one of them is not making a good connection until it heats up and expands enough to complete the connection.