Using Sublime Text 3, build 3111, on Debian 8 installed using the .deb package.

If you use the indent guide with any amount of line_padding_top, it seems like the indent guide doesn't match up with the line highlight as well as the caret.

Notice how the indent guide line extends a few pixels below the highlighted line. If I set line_padding_bottom and line_padding_top both to 0, this is no longer an issue.

EDIT: Ignore the text below, see comments

If I set line_padding_bottom and line_padding_top both to 0, I see another problem: Because I have caret_extra_top and caret_extra_bottom both set to 1, the indent guide is still 1px "below" the highlighted line.

The last image is obviously more subtle than the first... but if I move the highlighted line to the next line, you can see that unlike the previous line there is no padding between the start of the highlighted line and the indent guide. If the indent guide were 1px higher up, the padding would be identical on the two lines.