Hi Justin,
A few things to consider:
1) Digit duration on the voice port (timing digit 100) and for H323 (DTMF in ccm service parameters) should be 100ms. This is the standard and typically the default for FXS and will help the router better distinguish a actual dialed digit versus a fragment.
2) For MGCP, mgcp dtmf-relay voip codec all mode out-of-band should be configured so your not relying on a clean voice path to get digits there correctly.
3) For H323, be sure dtmf-relay h245 alpha-numeric is configured on the dial peer.
If none of these apply, please post more information about the integration.
Michael