I discovered the solution to my problem at http://ubuntuforums.org/showthread.php?s=ecc5815b2c7aab54acc6ec14a36364c6&t=196787
Similar to the mimetex.linux file getting changed when passing through a Windows world, somehow I had modified or opened and save the text file and introduced some dos characters. Installing the dos2unix and running it on the algebra2tex.pl file cleared things up for me.
Installing TEX, Algebra
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