I did scrape out the bits of caulk in the channels, there was not much, wonder if it was just some dots of caulk that were added. I would rather find glass a little closer to the width of the wood channel. See what I can find today.
Update, called same hardware store to see if they have different thicknesses and yes they do, single and double strength....yes strength, not double width. Double is 1/8" thick and exactly the size use in machine. I just thought glass was glass, now I know. Mystery solved.