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Thanks, @ldomaigne. The issue was actually that our custom board uses a switch which provides the ref clock to the RT1061. So, I changed ENET2 to receive the clock, and now the issue is resolved.

IOMUXC_EnableMode(IOMUXC_GPR, kIOMUXC_GPR_ENET2RefClkMode, true);
IOMUXC_EnableMode(IOMUXC_GPR, kIOMUXC_GPR_ENET2TxClkOutputDir, false);

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@ofirshe
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