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Its not the rail bolts. Its the sealant used to connect the roof to the body. In the corners, near the top of the windscreen, it tends to break away and leak. Clean it up with alcohol and cover it with sealant and you should be fine. I bet you can see the cracks in the paint.
With this starting after a new windscreen was installed I would still suspect the upper drivers side windscreen area.
Look at the corner of the body where the top drivers side of the windscreen sits, under the rubber there could be cracks in the welding/paint which can and do allow water in. The glass does not fill the entire area in the corner.
Test that area with your hose or some colored water.
Very common leak area.
Any sealant applied in the top corner between where the glass sits and the roof starts will block this leak.