In the spectrophotometric analysis(uv-vis-NIR) of ITO Nanoparticles in tetrachloroethane using a double beam instrument baseline was measured with 2 identical cuvette with solvent only. This gives me only negative values for absorbance. Does this mean there is significant difference in transmission between the blank and the reference even if they are the same compound?
Negative absorbance in a double beam instrument has no physical meaning because absorbance, by definition, cannot be negative. It ranges from $0$ to $\infty$.
Instrumentally, all that means is that somehow the sample cuvet is transmitting more light than the reference cuvet. In other words, the measured absorbance of the sample is less than than measured absorbance of the reference cell. Usually this can happen when the cuvets are not optically matched (i.e., they may look identical physically but their optical transmission characteristics are very slightly different).
Try swapping the reference cuvet with the sample cuvet and see if the readings remain negative again. If you are getting large negative absorbance values with the same solvent, try another cuvet set and if the problem persists, the spectrophotometer must be checked. However, if the negative values are quite small such -0.001 or -0.0002, this is tolerable and you can subtract the baseline from the measured signal in order to correct this systematic error.