Depending on what you are doing depends on how you can or cannot stop this from happening. If the parts are completely different then there is probably not much you can do, the replace algorithm is trying to match pins by name, but if you are replacing say a resistor with a capacitor you can alleviate this by drawing them in the same orientation, both vertical for example rather than one vertical and one horizontal.
If on the other hand you are using different symbols to represent vertical and horizontal orientations using say a resistor.1 and resistor.2 symbol, then you will have to live with the limitations or move up to the latest VX.2 release where we have addressed many of these issues.
If you are simply replacing one part number with another part number and not affecting the symbol then take a look at this posting replacing part in dxd to other part from data book with no change to refdes and look at the advice right at the end.