CLP automatically removes elements below the smallest element value from the A matrix by shifting all elements associated with the same column upward and reducing the length vector by one. Once an element is set zero, it cannot become non-zero again. This is a problem when coefficients between sequential solves temporarily become zero.
The current workaround is to set the smallest element value to zero, and let the Java interface handle values that are too small. With this workaround, scaling must be turned off, as long as there might be elements that are zero.