If you come off JB to go into self employment, and subsequently suffer a substantial loss of employment (ie, when the contract expires), you can apply to go back on JB. Because there hasn't been a break of more than 12 months, your claim is linked to previous claim and you take off from there. So for example if you had already exhausted 9 months of your JB claim, you will have another 3 months of JB left (provided you have the 260 stamps). When a claim is linked like this, you do not lose the 3 "waiting days" as essentially its the same claim.
If you have exahausted 156 days of your JB claim, and subsequently get another 13 Class A stamps (which you won't if you are self-employed), then you can requalify for JB after your claim has exahausted. This is a fresh claim, and you lose the first 3 days. Obviously you still need to meet the other criteria for JB (loss of substantial employment, sufficient contributions etc.)