I have been playing on Ygopro for a while now, and recently, I have noticed time has been set down to 60 secs rather than 180 secs. Combo decks such as Fire Fists and Dark World might have a problem with this since I am taking time setting up and my time is running short, too short for battle phase!. Is there a way to change it back to 180 secs? My rating is unnecessarily dropping very VERY low because of the timer.

Bigger problem!. My timer goes down on my opponent's turn!?!?! And I lost to time up!, On my OPPONENT;s Turn!?!?!
What is going on?!?!
You start with 60 seconds but you get bonus seconds after each move.
Basically you'll never run out of time during a long combo.
You can run out of time if you idle for more than 60 seconds.
I don't remember correctly but the hard time limit in the linux server is about 20 minutes per turn, 1200 seconds.

And yes, during your opponent turn you get 60 seconds per dialog box,
each time the game asks you if you want to activate a card effect you have 60 seconds to answer.
I doesn't take more than 60 seconds to answer a yes/no question.

check your internet connection, please.
The linux server is located in USA with a direct connection to china.
If you are in one of these countries and you still have lag problems I suggest you to test different network/router/firewall settings.

Thanks for the feedback

I get the bonus seconds part, but my time is running out while my opponent is carrying out his turn, No dialog box appears for this timer to run out.
Can you connect and play without issues on the USA/EUROPE servers?
on these servers the timer goes down on your turn too, but it's less visible.

You run out of time because of the lag between your PC and the linux server.
You could try switching from a wireless to a ethernet connection, this might help you.

On the USA/EUROPE servers, I can play without my time running out as fast. As I tried someone else's computer, it ran fine and could duel without running out of time. Thanks for the help.
I hate to reply to an old-ish topic but, my problem still isn't resolved. I have tried hooking my wireless computer to ethernet. After reading a few related topics, I found a Bandwidth test and this was my results:

0 kbps
0 KB/s
167 ms

Yet, My time still goes down during my opponent's turn, even on the first turn. Most of the time, it results into this:
Timing out? how did I time out?

Just to note a few things
It was my opponent's Main Phase 2
I have nothing on the field that would bring up a dialog box to activate something
If you bring up Hawk's effect, It happened during Main Phase 1 and I didn't activate it's effect due to time constraints, Otherwise, I would have set a Tensu to use my next turn

As you can see, My opponent was using an Elemental Dragon(Dragon Ruler deck). In which takes a lot of time to set up. When it IS my turn, I could set up, but usually, My time is too low to even enter battle phase or Main Phase 2 set up.

Any more valuable fix? My rating is going lower than it should. REALLY LOWER.
I changed the timing system to give more time to users who are lagging.
Apparently the problem is not your internet connection but your client,
from what I can see it takes a lot of time to get a response from your client after the server sent a request.
Have you tried opening system.conf and changing "use_d3d" from 0 to 1 or from 1 to 0?
What is your average FPS? (frame per seconds)

Currently, use_d3d is at 0 and my FPS at the menu is at 45-60. During a duel, it drops to 15 during duel. Even after changing use_d3d to 1, I still lose time during opponents turn. Could it be my low framerate? and If so, How do I optimize it?