I regularly use Sequence to make Dusk flats. It works well if you know what to do. A few points worth noting:
1. As soon as you check the "make dusk flats" box, a window will pop up asking for the configuration file which should be used (and which you must have set up previously). If the sun angle has reached 0 degrees, the scope will start to slew immediately after you select the configuration file. Therefore, you need to open the roof before selecting the file! Sequence does not automatically open the roof in this mode (for some strange reason....).
2. The START @TIME and RUN NOW keys play no part in taking flats. As already stated, the scope will start to slew as soon as the dawn flats box is checked, the config file is selected, and the sun has reached 0 degrees. (It would help if this was stated in the User Manual!)
3. The configuration file is set up under the settings window. The exact parameters will obviously depend on what filters are installed. In my case, I have L,R,G,B,OIII,Ha,SII. I find that for dusk flats the correct order is SII,Ha,OIII,R,G,B,L and the opposite for dawn flats of course. My NB filters are 6 nm. I find that if I set 5 flat exposures per filter the timing works well and I get a full set of flats.
4. Using a front illuminated CCD, RBI may be an issue. If you normally use pre-flash, you should turn it off for sky flats and then use dark optimisation for calibrating the flats. At least, that works for me.
Stephen