I have found that those bottles are not very air-tight and therefore allow products to thicken. I have had this happen to Collinite 845 and Menzerna 4000 .
If you squeeze the bottle firmly while the spout is closed, you will hear air being forced out between the neck and the cap. Placing a small piece of plastic wrap (Saran wrap) over the bottle opening before you screw on the cap will make the bottle more air-tight, but of course you will need to remove the plastic before using the bottle.
Although I like these bottles for products that I use often, I don't feel they are ideal for long term storage.