You are not clear about which box you did not check.  There are two boxes for this in ProConnect Tax:

Profile > AMENDMENTS > Federal Amended: This box should be unchecked as George suggested.  This doesn't actually tell ProConnect Tax not to generate a 1040X, only that it will not be e-filed;

Miscellaneous Forms > Amended Return (1040X)/Superseded: This box is what tells ProConnect Tax you are preparing a 1040X.  It needs to be unchecked so that a regular 1040 will be produced.