I have about 1,500 iPads deployed, and I have found nothing to suggest there is a problem with iOS that would cause that behavior. My first suspect would be a slight difference in the VSC or radio configurations or the use of non-standard characters or spaces in the SSID or WPA password. The commonality/non-changing aspect is the wireless configuration installed as a profile on your iPads. Since your controllers are not teamed, the configurations have likely been created manually on the different controllers, and that is a much more likely place for errors to have crept in.
Your users should not have to "attempt to join" the wireless network when moving from one building to the other, the devices should authenticate automatically and will reliably if the SSID configurations are identical and spaces and special characters are avoided in the SSIDs & passwords.
And easy test-- remove your main SSID from the iPad wireless profile (or create a new one) with a very simple eight character SSID (12345678), a simple eight-character password (87654321), and set up a new VSC on your controllers with the same settings, do not hide the SSID, set the network WPA2-PSK only, block out all but channels 1, 6 & 11, and no other special settings. Sync the APs and try moving an iPad or two between the buildings. I suspect it will work without needing to manually connect. If that is the case, then it is either a difference in your controller configs or the use of spaces or certain characters causing the issue, and you can work backwards to pretty quickly determine what it is.
If you determine that it's a setting you need causing the problem with the iPads, there is no harm in creating a dedicated iPad VSC. You can still set it to use the same egress VLAN as other VSCs.