Since you are in IT sector, I assume that your company is covered under the Shops & establishment Act. Even if it is not, it really does not matter.
Company is bound to disburse salary by 7-10th of each month and any violation thereof attracts penalty and interest. Since the company delayed in paying salary and also there was less payment, please demand the less paid amount in writing. Additionally you can also demand your travelling expenses in the same letter. You should keep an acknowledgement of such communications/ letter for future reference.
Asking anyone to resign is illegal and amounts to termination. There is simply no provision of "ask to leave" in labour laws. The company is simply threatening/ pressurizing you to obtain the resignation.
Submission of company's property takes place when there is a cessation of employer employee relation either by way of resignation or termination unless the company has asked you to refund their property for any other reasons.
If the company refuses to give you in writing to hand over the asset, then it is better not to. First ask the company to issue you in writing about handing over the property of company.
Only upon receipt of anything in writing, you can take any steps. Just on verbal communication/ threat, you do not need to do much.
But since the condition between you and the company has deteriorated now, always communicate in writing as far as possible (but make sure each and every word is chosen carefully)
9th February 2017 From India, Kolkata
And I am also curious as to why they have put your salary on hold.
It's better you give the full details rather than be happy to get a positive answer which may not really apply to your specific case
14th February 2017 From India, Mumbai