Android - ListView - if i filter list having checkboxes it gets me different values in array

I have a ListView which has around 7 items and 2 are checked like this:

http://ift.tt/19ADp6m

I'll check one more item in the list which is filtered:

http://ift.tt/1z0UZVX

Now i'll clear the filter and the result will be something like this:

http:// http://ift.tt/19ADrLn

But when I add these items to array it stores wrong values due to filter option.

Can anyone help me for this?