set_clock_groups not being applied to pll clocks

You need to explicitly add the PLL derived clocks to the groups as in:

set_clock_groups -asynchronous 
    -group { 
        adc_clk 
        the_adc_pll|altpll_component|auto_generated|pll1|clk 
        the_adc_pll|altpll_component|auto_generated|pll1|clk 
        the_adc_pll|altpll_component|auto_generated|pll1|clk 
    } 
    -group { 
        sys_clk 
        the_system_pll|altpll_component|auto_generated|pll1|clk 
        the_system_pll|altpll_component|auto_generated|pll1|clk 
    }