Do your transactions include fees? Zero fee transactions are not relayed by bitcoin clients if the memory pool is filled with free transactions. I personally set my bitcoin.conf settings for free transactions to a low level to discourage free riding.
Since Mt.Gox is known to never pay fees, the effect you are seeing is likely the result of Gox (and others) triggering automated house keeping transactions at the start of each day.
Right now, I have the following settings...
limitfreerelay = 5
blockprioritysize= 1000
I usually add the fee recommended by Bitcoin-Qt.
Could you please recommend me where can I read more about fee settings and fees?
Sometimes faster.
Sometimes slower.
You don't have to worry about the exact time for transactions every time.
The most important thing is these transactions are finally confirmed.
True too.