Might be a false alarm.
When you made those recordings, did you press Record button before pressing Play?
If so, then you'd have some digital silence at the start of each WAV, and likely not the same amount each time.
That can easliy confuse shntool.
Shntool takes the first sample from the first file and compares it against the first sample from the second file.
They match-- both samples have a value of Zero (digital silence).
Likewise the 2nd samples from each file match each other,
and the respective 3rd samples match, etc. . . . because they're all Zeroes.
shntool would mistakenly conclude that the two WAVs are aligned, when they're probably not.
Later when it reaches 18% one file might contain Non-Zero data
while the other file is still silent zeroes. Hence the error.
Try trimming the digital silence from the start of each file first.
Actually shntool will presume the two files are already aligned, unless you tell it otherwise by using the "-s" option.
Then shntool would try to detect how much time-shift between files.
Not sure if xACT will pass that option to the underlying shntool, or not.
You could run shntool yourself from a command prompt, such as
shntool cmp -s Take1.wav Take2.wav
In that case the files needn't be perfectly aligned, but within three seconds (default setting).
Still might need to trim leading zeroes though to avoid a false positive as above.
If using xACT (presumably without the -s option?) then you'd have to align the files yourself before calling shntool.