if the tip is stored down i THINK the liquid ends up at the end of the syringe, if the tip is stored up i think the liquid ends up at the tip.
if its just on the shelf you could end up with a mixture of thermal paste and liquid.
i have encountered that problem but just wiped the cpu clean and tried again with better result.
however it takes ALONG time for it to happen, did a EXTREMLY quick googling on it earlier today and one fellow experienced the problem with as5 that hadnt been touched in 5 months.