I'm sorry that we couldn't provide a more definitive/exact answer for you as to HOW your wireless alarm system was hacked.
What I am giving you answers from is from my experience with WiFi that is used for wireless connectivity for wireless NICs. WiFi has many different forms of encryption, but only the latest WPA2 standard provides the best "anti-hack" encryption since it uses AES-256 encryption (http://en.wikipedia.org/wiki/Advanced_Encryption_Standard
The specifications for your alarm does not mention exactly what standard it uses to communicate between devices. Some forms of encryption can be hacked within minutes by using "freeware" readily available on the Internet (WireShark is a popular one) to capture wireless transmissions and track when/if data streams change so that they can attempt to figure out the encryption key interval, thereby being able to "mask" that their own device is sending the signal and not the "real" device. I would assume the same may apply to your situation.
What (or who rather) I would ask is:
1) why/how the alarm system manufacturer system was hacked
2) why their system is insecure
3) why the alarm system monitoring system didn't detect any changes
4) what kind of guarantee they give on their product that it protects home from burglary
Just about any wireless communication can be intercepted. If that communication is not encrypted or "masked" in some way or uses low-grade encryption, it can easily be hacked.
Some burglars already know the weakness of many security alarm systems. It's like a computer user: the savvy ones know enough of their way around, but them leaving a 9x9 patch of dead grass is a giveaway. The authorities (police) should be involved for investigation as well. That seems like very interesting evidence you have gathered on your own. Knowing what has changed makes a BIG difference, just like in the computer and networking world.
If this does not help explain anything for you or to your satisfaction, I can open this up for other experts to explain, or submit for you to be refunded.