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How often & how much are you cleaning? If you do too much that in itself will stress her out & she'll associate the box or tube with stressful things so do try to keep cleaning to a minimum, spot cleaning daily then maybe just do partial cage cleans when you need to & not all of the cage at once.
If you can leave the box in the cage or just use it to hide treats in when not cleaning making it more of a game she should be a bit happier to continue going in.
How long has she been acting like this? Even after being a bit stressed out they usually settle back into previous habits again with a little time.