Superscript or subscript formatting will affect the spacing between lines on a one or one-and-a-half line spaced document. This also occurs in MacWrite II (all versions). Both programs are shifting to accomodate the height of the character being formatted. If the formatted character is in 9 point size, the only workaround is to use double-spacing between lines.
In ClarisWorks 2.0 and higher, a better workaround is to switch the paragraph formatting from lines to points, and then adjuct the point size as desired.