There will not be a specific reasons. You have to optimize the either the method of preparation, or the core-coat ratio or both. This is trial and error. Usually emulsification methods give less encapsulation. Best one has to be considered as a optimized formulation. Refer related literature, it may help you in this connection. Please upvote my answer.
I would recommend to try MPs, In that case, You can sonicate protein in oganic phase to disperse and then add to the external aqous phase (O/W). You can get high encapsulation.
TiO2 (JRC) was suspended in physiological solution containing 10 volume % of rat serum (Sigma) and sonicated (Dynatech Artek 300) for 15 min. in a tube with diameter of 9 mm, at 150 W. Analyses of size distribution and pH of NPs was done in Venice (by equippment NICOMP 370). The size distribution was bimodal, with peaks at 84 (±8) and 213 (±15) nm. pH was 7.5.