As part of the punishment process, whilst you are jailed any stacking effects given by tokens will be nullified. So anything you may have saved up (energy, mythril turns, faith, wraithblade touches etc) will be subject to the reset rules of any normal, non token using account. This means simply, that energy will be set to half at main rest, you can only have 2 wraithblade touches and 2 mythril turns. Whilst some may find this an unfair punishment to go with the whole being locked out of your account, this, along with other punishments (in cases where illegal funds are involved, they will be removed from the player and the game, loan defaults mean the full amount will be removed from the player minus any payments made and so on) the reason you get this further punishment is simple: To make you want to follow the rules fully and never lose out on these things again.
Every account which gets jailed and is subject to the aforementioned punishments. However there are times when a jailing was given for security purposes (suspected hacked account for example) in these cases, we may reimburse the items lost, or more likely reimburse the items you would have gotten. For example: You are jailed 5 days for investigating a possible hacked account, the result is you were hacked and we will sort out your password details with you, and release you from jail, reimburse you the 5 days of items (so essentially 10 mythril turns, 10 wraithblade touches and a sum of energy). This is a rare occurance but is currently the only way an account is entitled to a refund of items other than in a case of a management mistake.
Jail is used to punish offenders and also as a device to encourage people to follow the rules more closely. If you find yourself jailed at some point and lose out on items, hopefully that time spent and assets lost will cause you to want to be within the rules at all times so as to never lose out again.