Unfortunately some Ikea shelves appear more prone to a degree of warping than the table tops. I found this out on my current cameo which uses an Ikea shelf, where after I had screwed & glued a painted plywood board to the top and laid some of the trackwork, I noticed the centre of the board had bowed upwards by approx. 5mm.
In an attempt to overcome this, I made four cuts through the shelf's bottom layer at equal distances either side of the high point and clamped it to a table using sash clamps. When the board was removed after a few days the bowing had reduced to 2mm, which I deemed to be acceptable and the cuts were filled with waterproof PVA in an attempt to re-introduce some strength. I have since beefed up the layout facia material to help stability. So far operation of locos and rolling stock does not appear problematic and buildings have been designed to ensure they are horizontal.
Hope this may help.
Vaughan