So why does it matter if they have two different versions?  Because the version that is used by default is version 5 and about 6 years out of date.  The biggest loss is no sepia toning in the old version, but as I found out this morning the old version also doesn't work well with watermarking.  Instead of overlaying a transparent PNG like it should, version 5 just puts a semi-transparent white box where the watermark should go.  Obviously not the correct look.

Up until today I've always recommended GoDaddy users change the setting on Options -> Images to use the GD library instead of ImageMagick.  But with version 6 also on their servers you really should be using ImageMagick. 

Fortunately it's an easy change to make.  On the Options -> Images tab you'll need to make sure that the dropdown next to Image Conversions is set to ImageMagick.  Then set the ImageMagick path field to /usr/local/bin .  It may have been /usr/bin which is the path to ImageMagick 5 or it may have been blank.  Either way it was using version 5. 

Here's a screenshot for the visual learners among us.