Can an ARINC 429 controller set to receive messages on high-speed (100kHz) see 12.5kHz messages?
That is normal for an ARINC 429 receiver. The clocking for ARINC 429 is built into the transmission data, with the bipolar Return to Zero format having a Null for the last half of each bit time and requiring 4 bit times of null (0) voltage between labels. This lets the receiver adjust to the data rate automatically.