They differ in the way they sound; they're actually different letters. Check this consonant table, there are two "ta", one in row 3 and the other in row 4: http://www.languagereef.com/consonanttable.php?lang=SANSKRIT

This video shows their pronunciation: http://www.youtube.com/watch?v=y8GhoAIAtt4

This structure is same in all Indian languages.

Could be that they are different Sanskrit characters without similar notations in English?

I presume it's a tonal language (like, say, Chinese), where words have different meanings depending on the gone that they are said in.