Yah it does. If your looking at your system after its been running a while, on an automatic program. As compared to walking up, and manually turning it on,when its been off for hours.Your well has recovered.
example: Your water table is 22',when you see it after it has been on for 2 hours,the water table has dropped. When you go out at some random time after the well has been sitting,off,for a while. The water table is back up where it usually is. You should try to manually bleed on a valve,and let it run for a while. or ideally,shut the clock off during a cycle when it is looking crappy,and then try opening a valve,if you are running dry,it will not look good,just like it doesnt when its running a program.
Its not the end of the world if you need recovery time,it sux ya. I just went to a house a couple weeks ago. It does the same exact thing that yours is doing. Brand new goulds submersible. thats probably why too, hes got a giant pump,when its been off a while,then you turn it on,its absolutely cranking, but it also takes about 5 minutes to suck the water table down X amount of ft. The easy solution,is delays between stations,it allows the pump to recover. Some pumps get so bad you need 4 start times,10 minutes rest between every zone,and every zone running a little more than a quarter of a normal run time x4. but thats what needs to be done,short of going deeper. good luck. It could also be somthing else of course, but if your turning the valves on after the pump has been off,its most likely running dry. If it looks crappy from the clock,then you shut the clock off,and go bleed on a valve,and it works great thats totally different,and strange.
Let us know if it looks crappy from the clock,then looks good from the valve,right after you shut the clock off. Then we'll give you some more ideas and things to try.