i think it goes in alphabetical order, probably more like ASCII order though. i think the only way around this is to name your files with the date preceding any other attributes of the file... for instance i have SGP configured to name my files thus:
tmb_ori_m33_Light_B_2016-09-27_000457_0600s_bin1x1_sky_1.7deg_rot_355.6deg_B.fit
so telescope, target, type, filter, date, time, duration, bin, rotator angles, filter (just makes it easier visually to see the filter there on the end.)
so in my case i wouldn't be able to have files with different filters be shown consecutively in Blink as the filter name takes priority in the grouping.
it would be nice if the order could be specified somehow... blink was written by user NKV who i don't think we've seen around here in a very long time. i guess juan has the source code though.
rob