Hi Adam
what clock had you checked and what environment?
It may be recommended to check that on bare-metal tests SDK
i.MX 6Series Platform SDK Bare-metal SDK for the i.MX 6
power_modes_test.c, also there is simple gpt test (gpt.c).
Note, for example linux uses gpt as system timer, also it uses
24MHz clock which is not gated by CCGR registers
ipg_clk_root by CCGR1[CG10],
ipg_clk_highfreq (perclk_clk_root) by CCGR1[CG11]
Table 18-3 IMX6DQRM
Best regards
igor