I don't know what is causing your problem, but if commenting the lines, re-running, etc works then try the following:
1) Go to Project>YourProject>Make
2) Add "LineProblem = 0" without the quotes in the Conditional Compilation Arguments textbox
3) Bracket all your Form1.Line... lines with conditional If/Else as follows
#If Not LineProblem Then
Form1.Line (1, 1)-(1000, 1000)
Form1.Line (1, 2)-(500, 123)
#End If

Then when you want to "rem" the lines, just change the Make parameter to LineProblem = -1 (or any non-zero value), and the problem lines lines will not be included when the program runs.

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Marty
What did the fish say when it hit the concrete wall?
> > > > > "Dam!"