When it comes to wireless, anything metallic (i.e. trucks, flag pole, building structure material, other antennas) will most likely affect the performance and stability of the connection. Also, if the APs are behind a wood or brick building as well, this will also degrade performance and stability as well.
If the wireless access point you are referring to is the DWL-2200AP, that might be your problem. Some of these cheaper wireless access points are not really made for commercial application and deployment needs. If reliability is of a concern, I recommend looking at something like a Cisco Aironet instead (i.e. 1250, 1240AG) as these were designed for performance and stability.
A couple of other options: Hire a RF engineer to survey the area between the buildings and rule out any other possibly radio frequency issues that you might not be aware of.
Another option: Do you have something like a VPN tunnel between the two wireless environments? If so, some VPN endpoints can be set to aggressive mode and also have a heartbeat monitor to send a ping message back and forth over the connection to keep the channel open and operational.
