I do not see a switch happen, if it does the frequency is still at 125 MHz. Here's the generated MMCM from top.v:
MMCME2_ADV #(
.CLKFBOUT_MULT_F(4'd8),
.CLKIN1_PERIOD(8.0),
.CLKIN2_PERIOD(8.0),
.CLKOUT0_DIVIDE_F(4'd8),
.CLKOUT0_PHASE(0.0),
.CLKOUT1_DIVIDE(2'd2),
.CLKOUT1_PHASE(0.0),
.DIVCLK_DIVIDE(1'd1)
) MMCME2_ADV_1 (
.CLKFBIN(mmcm_fb_in),
.CLKIN1(txout_buf),
.CLKIN2(bootstrap_clk),
.CLKINSEL(crg_o_clk_sw),
.RST(crg_o_reset),
.CLKFBOUT(mmcm_fb_out),
.CLKOUT0(mmcm_sys),
.CLKOUT1(mmcm_sys4x),
.LOCKED(mmcm_locked)
);
Based on this I'd think we run at 125 MHz instead of 100.
I'll be happy to get in there and fix this, submitting a patch when I'm done. But since I'm new to Artiq I wanted to check in and make sure I'm not missing something.