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This is probably due to the fact that unpowered RTM will block it's I2C bus branch. The RTM 3V3MP is switched. Theoretically it's I2C could be switched as well.
According to mTCA 4.1 specification RTM I2C bus should be separated by bidirectional buffer powered from P3V3_MP (REQ 3-7).
RTM I2C pull-ups should be present only on RTM module, according to Figure 3-1.
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