The Heidenhain ERN1387 and Hengstler S21 are generic incremental encoders that have 1Vpp sine wave incremental outputs, unlike the more common 5 VDC HTL/TTL square wave output. These 1Vpp encoders often test well on the TI-5000JX but sometimes cause run issues on the TI-3000JX. The major culprit to the run issues is the low level, oddly shaped index pulse. The TI-3000JX run test environment is always slightly noisier than the TI-5000JX because of the higher voltages used on the AMC amplifier, and the noisier environment can cause the index to be read incorrectly, causing run problems.
Below are waveform diagrams for both encoders. Notice how the index signals listed as "R" (index, or Z pulse) don't have a clean square wave output. Instead there is a low voltage signal with a triangular shape. The only way to potentially clear up the run issues is to have less noise in the run environment. Make sure all equipment is well grounded, especially the motor, and make sure to keep feedback leads separated from the power leads. Unfortunately there's not much we can do if these uncommon index signals do not get detected correctly by the TI-3000JX.
See more details on testing these encoder in this article: https://support.mitchell-electronics.com/hc/en-us/articles/4409340233371-Siemens-motors-with-Heidenhain-ERN1387-or-Hengstler-S21-encoders
Heidenhain ERN1387 Waveform Details