Matt, new at this my self. I also started cukes indoors. When did you start them? For me it's been about 2 months and only transplanted them once. From small peat size pot to 6 inch pot. they're about 5" now. Maybe they go into shock from being transplanted so much
What kind of lighting are they getting
How often do you water? Me once a day with a spray bottle. Like I said I am also new but these are some of the things I do.