A number of things will change the boot sector (almost any program or bootable disc is a possible culprit.) That includes any O/S installation, such as Linux and Windows. Some viruses, worms, etc will also do it. It could also be done by security programs such as malware scanners (for boot time detection), backup/recovery programs and firewall programs, though those will usually use O/S hooks, not the boot sector. If the partition table is changed, that could also show up in the scan.